I'm hoping for crown authority to be significantly harder to raise especially the larger your country is (absolutism in England is about 50 years after the game ends, in France it's still 200 years away; for the empire it's never), and for it to have worse consequences.
Also if the ck2plus faction system revamp could make it in the base game. And for riverine provinces to get flagged as coastal (or a riverine flag) for the purposes of trade and city buildings, at least along major rivers like the Rhine, Vistula, Seine, etc (likely not the Loire, which wasn't navigable past Angers at the time).
Every lithuanian/prussian/general baltic province needs at least one more holding and one more slot at game start, or some way to survive. Similarly, because african provinces are so few, it would probably be best if they had all seven possible slots; I can't remember if this applies to vanilla CK2, but in CK2plus, both subsaharan empires are impossible to form without going on a rampage in North Africa.
EDIT - Ships excluded from the retinue manpower count. I can vaguely live with higher end units getting cut off for manpower count, but every single ship the retinue count removes is the equivalent of 75 knights in vanilla and 10 in ck2plus when converted to maintenance costs, and it's not like fleets are that huge.