Ah, well, I don't really have a personal favourite between the two really, I like them both! It does depend on each situation you're encountering though. Like the Acro Bike has a trick you can do to find pokemon in an unlimited time in the Safari Zone back on R/S/E, where you can just hop in a grass patch in one place, and you'll still be able to find pokemon! Plus, I think you should have the Acro Bike to explore more areas in the Safari Zone anyway~
Mach Bike is definitely great to boost speed, and I remember trying to beat my own time in the Cycling Road, hehe. Oh, and the Sky Pillar. Mach Bike is important for that too. So all in all, I'll be more likely to switch between the two. As for the secondary question, I think they'll most likely keep the functions, but hopefully they'll have the Acro Bike have more tricks! And keep that hopping trick that still encounters pokemon, ohoho~