I'd like to see Nexon implement "area rewards" for clearing the last quest in a string. Basically, give players Maple Points or Cubes as a one-time thing when they finish the entire questline of an area. That would encourage players to do more of the quests and storyline. (For instance... even your most endgame player might be tempted to visit a revamped Neo City if the last quest of it gave you some cosmetic opportunities or cubes).
Florina Beach just lost all purpose as a low level zone. Most of them did, but I liked how cute and whimsical the area was. It'd be nice if Florina became the starting area for Jett (with a revamp of course).
I actually like the new Kerning Square better for EXP purposes... But doing Blake's questline was pretty fun the first few times.
Chryse was annoying. I don't have any hard feelings to them changing it and relegating the PQ to the party quest area.
It would be really cool to see Neo City brought back and reworked. Being able to earn Android Hairs/Faces, Iruvata style items, etc would be appropriate there.
Make rings NX like the Nyan hat. +% EXP and Drop while on a map with your spouse. If married, you can TP to your Spouse twice per day.
And revamp Amoria PQ to make it Star Force and Arcane Power based on certain levels. Difficult but worth it and mix different game mechanics to make it a bit challenging. Have items include things like Onyx Apples, trait boosts, cubes, fusion anvils, crafting materials, recipes, etc.