You know, there are some things that are really important in writing (like research, which is something you seem to have done, and general originality, and readability, and so forth), but the most important of them is that you have to enjoy what you're writing. When you enjoy writing, it will show, and the readers will enjoy reading your story. So, when you think of things like this, the most important opinion is usually your own. If Pichu, Pikachu, and Raichu are your favourites, then write about them. Who cares if we've seen them being used in fanfics for years! If you're not copying any of those fanfics, it will likely be something new. If you want your trainer in Sinnoh to have Hoenn Pokémon, use whichever explanation pleases you most or happens to suit the story and the character. Evil team plots and romantic plots are probably equally popular and used, so you can choose whichever one you feel more like writing about: or, better yet, you can combine the two into a single story, like many people do.
Pokémon transforming into people and vice versa isn't all that common, actually, and it has a lot of unexplored frontier to be explored. Some people do pokémorph stuff, which can be pretty good and has a lot of room for darker themes, for example. Many people also use the plot from PMD games, which isn't necessarily a bad thing, but it does get old. You know, the whole deal with three-Pokémon rescue teams and so forth. If you want to write a fic like that, then go for it, but think a little first: will the fic bring anything new to the readers, or is it just the same thing than in Mystery Dungeon? If it doesn't bring us anything new, you should develop the story and reconsider some things about it before actually writing it. If you think you're on to something fresh and original, then go for it. Mistakes can be fixed later.
So, long story short: do what you feel is best. People are probably going to like a story that's well written and that the author loves themselves, as opposed to one the author writes to please their readers. If you write while aiming to have as many readers as possible, you'll likely end up ditching the whole project, abandoning the fic, and neglecting the readers you had. If you like writing the story, you'll stick to it until the end, and your readers will love you for that - you have no idea how many chaptered fics go unfinished. That doesn't mean you shouldn't listen to reviewers, though. You should definitely listen to people's advice and take note of it, but in the end, it's your fic, so it's your call. ^-^
I hope this helped!
