I just think the issue is the teams need a rework.
my biggest issues:
you're members were terrible to organize, as in chingling needs to have a list that you can organize as you want. I want my most used pokemon at the front and the others shoved away out of my way. and preset teams would be awesome.
the teams were hard to move through the dungeons at times. with 4 pokemon you're team often gets split up in the big dungeons and monster houses leave you fighting alone (they need to happen when you get tot he center of the room so your whole team is in on it.
your partner needs to be optional on early missions and changing leader too. yes I get it there is a plot, but training your team needs to be important. I don't want to be stuck with two pokemon, of which you only get 16 to pick from, as my main ones forever.
more recruit methods and not starting at level 1-7. recruited pokemon should start at higher levels even if they are from missions. they should scale based on the mission. eggs are ok though trading away your children is strange...
evolution early. I hate having an evolution one pokemon for the majority of the story I'd rather have all the pokemon be harder and evolution be jsut as important. maybe mid way though the first part (in comparison to PMD2).
I'd like to see more "starters" as in pokemon to become. just for more variety. my picks being:
gen 1: Cubone(bring back), abra (with the elemental punchs from breeding or somethign else for an attack)
gen 2: tyrouge, aipom, mareep, gligar, elekid, magby
gen 3 : ralts, aron, tapinch,
gen 4: none... they got all i wanted...
gen 5: roggenrola, sandile, litwick, golett, pawniard, and the starters of course.
yeah basically all my wants from the series.
Oh and a customizable base. I want to be able to put amenities in there like berry bushes, and seed plants.
DISCUSS, or if you would like I'll make this my own thread if you feel it diverges too much.