Fake Pokemon - Even though there's a couple of good ideas, and I used to make HUNDREDS of fake ones myself many many years back. I just... prefer the ones that actually exist. Honestly, there's nothing about your fake pokemon that makes it any different from the nearly 500 that's in it already. And most fake legendaries also just remind me of Sue characters. You like it, and you force it upon others and try to make it look "spesal"... But you don't really need it.
..... Which seems like an hypocritical thing when my game currently... has one fake. But it plays a very unusual role than.. well.. actually any other pokemon I've seen >.>;
Making the main hero talk - This has been something that's bothered me with every fake game(that does this). I prefer it if the main character just stays... silent. Because I don't know what it is but most seem to make the main character 1) a total jerk, 2) the typical spunky/headstrong/possibly sarcastic hero you see in 39672097.7 different games or shows, or 3) a goody-goody two shoes. And the worse part is, you're now stuck with that personality as you play... Where as in other Pokemon games, the person you play as is technically supposed to be a reflection of "you", to some extent. Even though you are still forced down a particular path.
I don't mind it in other RPGs.. of course. And there is ways to make the main character seem like it still has a soul, without it having a voice. It's been done many times before in games, and it's not hard to do.
Lack of Originality - I guess it's different if your purposely making a remake but... every fan made game looks exactly the same to me. I can't really stand it sometimes. Any game you see someone making its:
"You start off in the _____ region, on your 10th birthday Professor _____(insert name of a tree) allows you to choose one of 3 Pokemon: ______, ______, or ______ (insert the starters from either either generation), and are given your own trainer ID/license... as well as a Pokedex because Prof _____ needs you to gather data of every Pokemon you can find(because you know, their special Aides are too busy handing out items or whatever, and it's not like they asked hundreds of other kids do it too by now). And so you start off totally-not cliche quest to battle all 8+ gyms be the Pokemon Master! ... As if it hasn't been done before the last 80 times.
But along your way, you run into the evil organization, Team _____ (insert some sinister sounding word). They plan to capture the rare and powerful Pokemon ______ (insert the legendary the game is probably mascoted by) and use it to destroy/take over the world... Or, in story writer goes with Option B: Evil team has already caught/made an evil clone of said Pokemon and are using it right now. It is now up to YOU to stop them before it's too late.
And well... blah blah blah *put more things here, MAYBE one or two little things that could make the game a liiiiittle different from everyone else's*"
.... Well, alright. I have seen maybe a few ones that don't look too bad but... come on people, break out of the cardboard box. Most of the games I keep seeing are just "Travel to Kanto! Johto! Hoenn!" and like 5 other regions, rather than people actually trying to... well, add more quality to their work.
If you're making a Pokemon solely to unite all versions together, good for you(because I really do want a game like that someday). But if you want to make a brand new game... Please think of some brand new ideas first. Even if it's something that's never been IN a Pokemon Game before. Be a rebel >.>;;
Woah, this reply turned out extremely... negative o.o;