Her Colosseum/XD mixes are fantastic. It's too bad barely anybody touches those soundtracks way ahead of their time Pokemon wise.
But there is something I'd like to add from the plot aspect as well. Don't try to over complicate the plot. I mean having a more complex and convoluted plot can be more intriguing, but it can also lead to disaster leaving players lost on what's going on. When in doubt, always simplify it. I know you said nobody likes a simple cookie cutter plot, but even that can be enjoyable if it is well done and very well written. I know I'm going to get a lot of hate of flames for this, but Pokemon isn't the best genre for spectacular plots so going overboard will likely only hurt more than help. I'm not saying it's impossible though.
But yeah, I think I'll emphasize on the important stuff a bit more when it comes to the overall story section of making a game (since that is my strongsuit):
Setting: One very bad assumption here is that new region = better setting. While a new region may give the creator a thought that this is completely fresh and new, it's not. When creating a new region, it takes a lot of thought from the climate to the how the land form the people around them. Let's say you have this region called Ymora where breeding is so big that even wild Pokemon have Egg moves. This attracted a lot of strong trainers who are very competetive meaning battles take place there more compared to other regions (and People are snobbier as well). The vast climates also allow it to be a miniature bio-dome much like Hoenn. After you get a big picture, that's when you start breaking stuff down into different sections (as well as work on plot).
Characters: Often this and Plot go hand and hand with one pushing the other forward. Strong characters is a definite must for just about anything. Another bad assumption is that only the characters with unique sprites and are important to the plot matter. This is very, very untrue. Remember all those random guys standing around who all share one sprite? Yep, they matter too. I mean you don't have to do anything too special to them, but don't be afraid to spice it up and make them a little bit more than info givers and methods of experience. Reborn does a pretty good job which is better than trying to give examples.
Plot: I said it before and I'll say it again. Keep it simple. I mean it's almost a staple to have a crime syndicate, but there's so much you can do outside of "ermagawd evil team wants to use [insert legendary here] to create new/better world." Team Rocket and Team Cipher are some of the better main game villain groups and neither of them used legendaries when they first appeared. I'm not saying you can't use legendaries in the plot, but don't make it the main plot. It's a cliche for every Pokemon game ever created outside of a small few.
I guess there's one other thing I'd like to cover and it's just the battles/bosses. The difficulty is going to vary depending on what you're doing. Games like Reborn and Rejuvenation are going to be difficult because it fits them, but games like se7en are going to be a bit easier due to a focus of a fresh experience. There is such a thing as too easy (glares at gen VI) and being too hard. The mod I helped with called Reborn Hardcore is an example of when a game dances on the too hard line (it's challenging but right before the point of being unfair). Sticking generally close to the middle ground is where you're going to attract the most people, but if you're going to make it challenging, reward people for skill and strategy but don't force them to use insanely strong mons or cheap strategies.