(This post is geared toward Pokemon Essentials games)
Making a Pokemon Fangame is not easy. If you want to succeed, you must be careful, dedicated, and patient. If you have or can adapt to these traits, making a Pokemon Game will be much easier.
As a Fangame creator, I am currently working on my first project. I would say I'm about 50% of the way there, and that's saying a lot. There are lots of different jobs to do when designing a game, and they are time-consuming (well, most of the time)
Here are some tips:
1: Don't give up
There have been many times I want to give up, but you can't do that or you won't be able to make a game. You simply should calm down, take a break, maybe eat a snack or take a nap, and come back to your troubles when you can handle them. There are SOOO many things that can go wrong in your game. Pokemon Essentials is a wonderful tool, but it can be touchy. You need to be precise. You can't be making silly errors like misspelling Pokemon names or using the wrong image. There are more important matters to attend to. More often than not, you will be overwhelmed by your game. This has happened to me many times. As previously stated, take a break and come back later. Be persistent with your game (that doesn't mean doing it as fast as possible) and you should be good to go.
2: There is no rush
Unlike official Pokemon games, there isn't a deadline for your game. Fans may want it quickly, but take your time so you can make sure your game is as good as possible.
3: Be creative
People don't like copycats. Be creative with your game and make interesting maps and characters. This does NOT mean you shouldn't take inspiration from a pre-existing game. In fact, my game takes massive inspiration from Reborn. Reborn was actually the reason I started making a game in the first place. But that does not mean I am copying content from Reborn. Stuff like PBS files, Pokemon sprites and similar things can be copied since they're probably going to be the same anyway. It's just a way to conserve time. Usually, at least. Another thing to do is have interesting characters. They should have varying personalities, varying stories, and varying everything, really. And remember, using references doesn't mean you aren't creative. i plan to use tons of references in my game, and that's fine. I even plan to have a Pokemon World Tournament feature where you can fight rivals and gym leaders from other fangames. And that can't really be considered copying. Well, most of the time. It depends. But the point is, don't be a copycat.
4: Knowledge is power
Always know what you're doing before editing something. Diving in with no experience can mess up your entire game. (I found this out the hard way the first time I downloaded Pokemon Essentials and failed miserably) Before I tried again at making a Fangame, I watched tutorials. (They were by Thundaga. Great Tutorials. They explain everything so well. Give them a try on Youtube) Before, I said, "What the HECK is a PBS file?!". Now I have added every single Gen 6 Pokemon and all Gen 6 Moves. So yeah, don't mess with Essentials if you aren't 100% sure what to do. If you do, It may cost you your game.
5: Be truly dedicated.
There are two kinds of people that make Pokemon fangames. The people that have a vast knowledge of Pokemon and will stop at nothing to make a game for their self and others to enjoy, and the kid who thinks it would be cool to find wild Mewtwo and Rayquaza. My point is, many people start making a game and get disappointed when they realize that it takes lots of effort. But don't underestimate kids, either. I'm only 11. I'm not a veteran. I used to despise Pokemon until a couple years ago. Then I fell in love. But I'd say I've only been a true fan for a year and a half. Still, I'm doing quite well on my game and can tell my little sisters pretty much any Pokemon fact.
6: Don't use content made by others without permission
Some people are OK with you borrowing their resources with credit, but others are not. Always be sure that the the resources you may or may not borrow are OK to be used.
And those are my tips. Good luck to anyone making a Pokemon Fangame!