Hmm fangames that deserve to be advertised/talked about... I'm an utter fangame hound so this might be quite a large post, though story and aesthetic are my main thing and as a result I may gloss over or misremember details aside from those.
Complete (or near complete) Emulator Games
Pokemon Victory Fire, Pokemon Resolute Version & Pokemon Mega Power: These three games are by the same creator and it shows in both the good and the bad. Lots of inventive mon use and placement, fixed non-standard starters and interesting maps but English is absolutely not the creator's first language and it shows a lot. Also the early game tends to be hellish with trainers being overleveled initially. Difficulty past the start tends to be like official pokemon games and the story... Well the first two games, they did have plot but for the life of me I can't remember anything about them. Pokemon Mega Power on the other hand had a few plothooks that caught my attention despite the Engrish and references to the previous two games I didn't really get even after playing them but not exactly sure how the plot holds up long-term. I'd give them a 5 out of 10 with a recommendation to skip ahead to Pokemon Mega Power if the other two don't catch you.
Pokemon Ruby Destiny Series: Ohhhh these ones..! So inventive and clever! ...but so so buggy, and with plot important fakemon legendaries that have meh designs and make little sense.
As it may sound the Ruby Destiny Series likes to do its own thing, which for the most part is good. The first game, Reign of Legends, is basically a standard gen3 pokemon game with some lovely area designs and if I'm remembering correctly some gen4 mon, nothing too special. But the second game, Rescue Rangers attempts to be a pokemon mystery dungeon game complete with unevolving protagonist human-turned-mon. How well it succeeds is YMMV but at the very least I found myself sucked into the plot, wondering if these kids would ever return home... Right up until I found myself stuck in a rather nasty game breaking glitch and well that kinda killed that one for me.
It's the 3rd game Life of Guardians though that really shines Lovely area and character design, good music and plot~ Just feels something like a light fantasy story and left me completely charmed. Difficulty of all three games is fairly standard Pokémon but on rare occasions there'll be a nasty difficulty spike... Like an end game boss actually being Lv100, which makes sense plot-wise but odds are you are tops lv60 and not prepared in the slightest after how easy the rest of the game was.
Pokemon Gaia: Very good 'traditional' pokemon game. Starters are standard gen4 starters but the visuals are lovely, the mon in general carefully selected and it's just really nice. Difficulty is a tiny bit more than official Pokémon games but not by much. Also megas exist but I can't remember if fairy type does...
Pokemon Snakewood: This game is hard to describe. On the one hand lots of horror & fangame parody, dead baby comedy and difficulty, on the other hand... dead baby comedy done to cheery unchanged gen3 music, tiles and sprites, and the difficulty is less average battle and more desperately avoiding the surprise horrifically overleveled things that will wipe your whole team. ...Also the fakemon can be a bit meh. It's pretty fun if you can overlook the flaws but those flaws can really grate. ...Also the puzzles tend to be horribly hard and there is a section of game it is fairly easy to get perma-trapped in due to not picking up the easily missed HM-Strength from a rather irritating maze before ending up in said trapping area.
Pokemon TPP Anniversary Crystal: A rather tricky to find and little known hack of Pokémon Crystal by the Twitch Plays Pokémon dev team and the guy who made Pokémon Prism. Starts off in Kanto and at first you might think it's a standard gen1 rehash but the story (simple as it is) starts doing it's own thing from the S.S.Anne onwards. It is limited to the first two gens of Pokémon but includes quality of life improvements such as Fairy typing, Abilities, physical/special split, altered and some later gen moves for balance, altered BSTs (Parasect is OP), a move tutor that teaches tutor and egg moves, a guy who sells Master Balls, Battle Tower awards cash, non-stop bug catching contests, all existing mon (of every evolutionary stage) being catchable somewhere in the wild and plot stuff that keeps happening once you've hit the cap of Lv100 including stuff that only unlocks after you've completed the dex, and there's also an optional custom AI program that be installed to make opposing trainers harder (though YMMV on how effective it is VS how much effort it is to set up). Oh and there's also one well designed fakemon but you need to use a distribution code to get it and those only work after you've filled the dex so... Yeah. Optional. Heavily recommended game if only because of how beautiful all those revamped Gen2 style moving sprites are.
(I also recommend playing as a boy if you want better rival dialogue and to look up the fanart and comics done for the actual TPP run of the game. Some of them are just marvelous Praise Lord Amber, EvanXAzureOTP) Esentuals Kit Games
Pokémon Present: This one is actually one this site and I really, really recommend it if you love plot, characters getting slowly fleshed out, mystery/lite-noir or puzzles because the whole game is centered around those aspects. Sylvester is fun main character, Truffles is best mon and Mordicai eee Just play it, the current 8 case demo isn't a whole lot but it still kept me hooked for the better part of a week and I look forward to the next update.
Battles can be quite difficult as mon selection is fairly limited and you start out with ice types but it's not Reborn level as most of the difficulty is in finding that last bit of evidence or working out puzzle solutions. There is a level cap but it took me quite a while to notice it, I recommend testing right away to see if you're one of the unlucky ones whose computer crashes trying to load the game after saving in L or Full screen, and worded to avoid spoilers: after you beat a powerful lady and have to check her establishment, take your items off your mons as the upcoming plot thing eats them. HAs and visible IVs are a thing.
Steve the Bibarel series & HITMON JAM: Short, comedy games. Very simple with the player only controlling one mon but I personally hold Hitmon Jam as one of two games I must insist people play at every opportunity if only for the laughs.
Pokémon Edge Rising: The other fangame I must insist people play for the lols. Edge Rising is a parody of edgy Pokémon Fangames tropes including disturbing fakemon, insane regional 'history and practices', badly written backstories, non-sensical character motivations, 'trash' starters, cutscenes that go on for far too long and whole sale referencing to other video games. It's a beautiful thing of a game and I legitimately recommend playing its 9 or so hours of gameplay if only so every time you see someone recommend Dark Rising you can think of this game instead and start snickering.
Pokémon Black Cinder: English is clearly not the first language of this one's creator but if you can overlook the Engrish and other 'lack of polish' details this clearly unfinished game has, you might find it a lot of fun. There is something around 17 or so starters, some of which are standard some not, determined by a personally quiz. A strict 'you can't level beyond this' level cap system. Tough gym leaders... The real draw for me though was the atmosphere of the plot which I'm finding really hard to put into words but there was one segment I had to play as someone other than my main character and the music and area design along with what happening in the plot was just. Just really great It has a LOT of rough edges though (like some areas being so large the game struggles to handle loading them, unfinished sprites, etc) and I have no idea if it'll ever update again.
Attack On series: Two short Pokemon fan games not about badges but about characters fending off danger. Attack On Silph Co and Attack On The Space Station are both fairly simple gameplay wise with the standard difficulty being a bit harder than official Pokémon games but nothing needing exact natures or EV training. It's hard to explain why these two are so good but... I really like how they did the story I guess. Also Pokémon in space is criminally underused by fanworks and AOTSS does it well Pokemon Police Force I think is by the same person and if not, good for the same reasons.
Pokemon Twilight: Another short, really good one. Plot is kinda alright I guess but it's more the mon selection and difficulty that drew me to this one. Also newer mon like Grumpig being done in that colorful jagged gen2 style It's been... A long time since I've played this so I don't remember a whole lot but it was a nice challenge (again nothing on Reborn level) for 12 hours or so and I really liked the aesthetics.
Full Moon: I wouldn't have mentioned this one if it hadn't come up prior on this topic but... Full Moon has some really, really great things and some really really awful flaws holding it back. Greatest thing it has is that the locations of the game are beautiful. The towns, the caves, the flowers and scenes of war in the ancient past... It's very inventive and those things kept me invested for a long time. ...Unfortunately that was all that was keeping me invested for a long, long time - the plot reads a lot like someone's first fanfiction, a romance fanfic at that. Initial descriptions which lured me to it, were some unknown persons claiming the game was 'backstory of Reborn's Luna' and yeah no only thing they have in common is a game sprite and name. To give an idea 'Luna' of Full Moon is easily lured into relationship by former bully via one line of dialogue despite being a very reactive teen in ever other scene and the vast majority of the story I remember revolves around the drama of this clearly very important and heartfelt 'love' in-between the 'events that could drive them apart'. Add in angsty reasons for 'totally former bully and now super handsome bf' to go angst about, teen drama like some of the more frustrating parts of Rejuvenation but much less of the skill for writing them and agghhhh.
Mon difficulty might've gotten better since I last played but I remember it being inconsistent, more on the easy than the difficult side. Music is GlitchCity and therefore fantastic.
Basically if you can handle the... Plot, there's a lot to like. Especially during the time hopping segments. If plot is a thing you even remotely care about the game can be torture (of the kind that leaves you feeling guilty because it's clear the creator put so much love into programing these really amazing cutscenes and stuff for it but because the writing is still 'first fanfic EVar' that just makes it even more painful and... Maybe it's gotten better since Ep8.2 but I don't know if I could bring myself to find out).
Pokemon Zeta/Omicron & Insurgence: As fangames good they're alright, biggest issue is almost everything they do, Reborn, Rejuvenation and Desolation do better outside of custom things like new megas, delta forms, and nuzlocke/randomzer options. Their plots are... Egh. Insurgence's can be fun but the 'dark' moments tend to be fairly clumsy and forgettable, and it probably says bad things that even after playing it several times I can barely remember what the main plot is compared to a few 'subplots' that pretty much get ignored or dropped 2/3rds of the way in. Main reason to play them is those custom game mechanics and yeahhh Zeta and Omicrom really haven't aged super well. Still very solid fangames though and I loved having Mega Marcargo with Storm Drain, a Christmas Misdreavus and a Levanny wearing armor. So cuuute
And that's all for now. There are several others I'd like to recommend but they've either already been brought up or they are obscure ones I think I'll need to refresh my memory with a replay before I do so (to make sure they're actually as good as I remember) and that'll take a while since, well I'm finally going through Reborn episode 18 (I wanted to wait until 19 but TTar's nuzlocke broke my resolve by reminding me how much I love it) so yeah.
Hope something on this list helps you out. /