I'm slightly afraid that they'll change only aspects of vanilla Smash 4, and strong customs may then become overpowered. For instance, they could buff DK or Wii Fit Trainer quite heavily while leaving their strong customs touched, creating an overcompensated character that may (or may not, depends on the extent of changes) be overpowered. Of course, they did balance customs in 1.0.4 (or 1.0.1 on Wii U I think), so it's probable they'll keep customs in mind when balancing. The other character I'm worried about if they don't touch customizables at all is Mii Brawler. If every other top 10 character gets nerfed and Mii Brawler remains untouched, I feel small/thin Brawler would be overpowered in this situation, and I don't really like a Mii Brawler centralized meta.
I would be pretty sad if we were moving towards a customs meta, and then Nintendo balances for a customs-less meta. I feel like it would create an even greater rift between communities and start up more debate. Hopefully that doesn't happen.