There is a lot of stuff they could improve:
"Spinda effect" eggs: all eggs have a random pattern of spots and colors. Almost no egg is the same.
Return of HM dive: Also, randomized dive areas with a fossile to be found there and rare pokemon. Also underwater caves like the Team Aqua cave, just as a natural cave where many secrets can be uncovered.
Just new pokemon in the regional dex: Rather make old pkmn available once you get nat. Dex.
Legendaries: only new legendaries available. Dont care about how many. Many legendaries: more choices for battle, which is a good thing. If you dont like legendaries, just Think of em' as normal pokemon with a cool ability, much like Wonderguard. Nothing force you to use them...