I don't think most of these would happen, but everyone can wish, right?
the ability to move moves around again!
I want better dialogue with the extra's.there should be a few phrases they have (maybe not for all of the extras, but at least some) For example they could say
oh! my friend also has *insert pokemon at the head of your party*
Yesterday I heard you won *insert badge* etc
I want detailed sub-plots.They should be optional though.
for example, A scientist is investigating the differences between pokemon of the same species. he needs x amount of pokemon raised to x level. When you do that, he then wants to see the difference between trainer raised pokemon and a daycare raised pokemon. Then maybe he wants to see how much happiness (or lack there of ) effects return/frustation. Etc. But I don't want it to be, hey you did one thing for me, here have a gift and then I'll say the same message over and over.
Maybe a ending to a mission like that could be "Thanks! I think that I know everything I need. I'll ring you when I've analysed the results" when he has analysed them, they could say "Hey! remember the experiment you helped me with? well it's nominated with for a prize! if I win, you can half of the prize!" then afterwards it'd be "Guess what? I won! The prize was 10,000 pokedollars, a 10 rare berries and a fire stone. Here, have 5,000 pokedollars, 5 berries and you can have the fire stone, i have no need for it"
Other missions could include mentoring younger trainers, protecting places, doing errands for people.
There also should be a way to keep track of what you've done, like a sticker to put on your trainer card or something.
I realise that things like these are already in the games, but I find them lacking. I'd like them to take awhile.
More family involvement! Though now the character is older, it's less likely to happen. Maybe your mum (why is it the mum is the only constant family character? what about siblings, aunts uncles fathers? I know not all kids playing have dads etc, but I don't see my dad a lot and I still find it's strange in all of the games, only one has a dad in it ) Will call you when you enter a town and say something like "Oh, you're in *insert town name* your uncle lives there! pay him a visit."
If there is something like the pokeathlon, you could train your pokemon, which would raise their stats. not just rely on aprijuice/poffins/etc
Also when you walk up to the house a door could appear on the bottom screen and you tap it. Some wouldn't open, it'd say something like oh... it appears the people aren't home. I think it would be better then having houses without doors >.<
And another thing that annoys me is everyone in the game assumes you look after your pokemon well. I think pokemon should have some kind of upkeep. IE, the pokemon in your party need brushing every so often or their happiness drops. And if you don't brush them, other people will comment on it. Maybe introduce health issues too? like toothaches, flu etc, They wouldn't happen a lot (maybe a average of a problem every ten hours played) and it wouldn't be caused by battles. You'd take it to the poke centre and they'd give you medicine that you should give once a day for X amount of days. While it is sick it might only have 3/4ths of it's HP.