These suggestions would totally change the Pokemon franchise for the worst. Most of these ideas don't make any sense at all.
1) Character customization - This worked in Battle Revolution because we could see are character in full 3D detail throughout the battles. However, customization for a tiny sprite that would be very difficult to even notice? Not needed. Also, a facial hair option?! Most Pokemon heroes are only 10 years old, and even in Black and White they're only supposed to be around 12! (I think...)
2) EV and IV - This is what makes each Pokemon unique. If every Pikachu knew they same moves and had the same stats, the battles would be pretty much decided before they even began because your opponent's moves would be easy to predict. I personally don't EV train my Pokemon, but I think getting rid of it would take all the fun away from training them.
3) No more Pokemon - Why not? There are countless animals on this Earth, with some just waiting to be discovered. (even more if you count plant life). There's no reason that the number of Pokemon should be limited. Also, at this point in time, there is no need for an "Anniversary Edition" because we already have FireRed/LeafGreen and HeartGold/SoulSilver. Why would GameFreak keep remaking the same games over and over and over again? I can see a remake of the original Red & Blue/Green possibly happening again in the future, but not anytime soon.
4) Remove Breeding - Same as the EV and IV issue, removing it removes the tactical aspect of the game.
5) Custom Gyms - Why? Gym Leader is a lesser title than Champion, and even more so than Pokemon Master. Why aim for a lesser goal? And simply running a Gym would not offer any form of story. How would you advance in a game from this? While the idea is interesting, I feel that it sounds better than it actually would be, in a "too good to be true" sort of way.
6) Less story - This is the first case I've seen of some complaining about TOO MUCH story. Most story-based complaints I've seen are that they don't have ENOUGH story! Black and White had the best storyline in my opinion, and every new Generation seems to be better than the last. And saying that Pokemon should be more "realistic" is just plain odd. Pokemon has never been, nor will it ever be realistic.
7) Custom PokeBalls - This has been done, but how would it make a real difference anyway? There's no practical use for changing the appearance of PokeBalls.
8) Co-Op - Again, has been done, but there is no need for it to be necessary in completing the story. Also, trading can be seen as Co-Op in a way.
9) "Caught 'em All" Reward - Catching all the Pokemon IS the reward. You get some kind of special notification for doing it, but the real reward is having data on ALL the Pokemon, which is the goal the Prof. gives you at the beginning of your journey anyway.
10) No Backstory - There was a backstory? The backstory for our characters is that they are beginning trainers that agree to help the Prof. study Pokemon. That's it. There story builds from there. Rival development? Remember that "we" are the character in the game, not ourselves. Our rival is who our character sees as a rival, not who WE see as a rival.
Overall, none of these ideas would have a positive affect on the games. Most of them are awful ideas.