I'm happy with the emulation quality of everything on Wii U and 3DS except the blurry/dark state of NES on the former. It's just painful to look at and really needs to be fixed.
Feature wise I'm fine with one save state and suspend states. 3DS GB/GBC/NES could really use button config patched in though, and not allowing color output options for GB games makes zero sense to me (especially when SPD went out of their way to deliver that optional pea soup filter), but those are the two biggies. Other stuff like online play or scanned manuals would be great but I'm trying to be realistic here. Oh, and obviously they need to do something about Super FX games still being a no show and some sort of price incentive for 3DS/Wii U crossplatform.
In terms of future platforms, I'd just like the promised N64 stuff on Wii U and I'd really love to see Virtual Boy on 3DS. I've made peace with not getting SNES/GBA on 3DS or Gamecube on Wii U. Right now I'm really much more concerned about 3rd party platforms on either than anything (TG16/CD, MD/CD, SMS, NeoGeo, NGPC, MSX, Arcade).
The biggest issue with VC right now isn't about emulation, features, crossbuy or even platforms really. It's content. Zero to two games a week per platform simply isn't enough, period. We have an insane western backlog that's just growing by the week and honestly even the fuller Japanese library lags where VC should be today. We should've improved from Wii, not gone backwards.