I remember at least two interviews with Nintendo executives in which they that no improvement will be made to the games. So definitely no.
They might bump they resolution though, as they did with the Zelda emulation on GCN. But as somebody already mentioned you can't improve the framerate with emulation.
Bumping resolution alone doesn't do much for those old games (especially bumping it only up to sd resolutions). Nothing for 2d games, little for those low detail 3d games.
Now better filtering would be nice. Trilinear + anisotropic + 6xAA for 3d games, and something like a super eagle mode for 2d games. No way they'll put in any 2d filtering modes though. (even for snes games which don't have the flickering problem of the nes)
If I wanted to play Mario64 or Zelda64 at high resolutions and tons of AF & AA I would just use my PC. There are already perfect emulators for these games.
Don't think they're quite perfect yet, or ever will be. They generally still have small glitches here and there, I'd imagine that the Virtual Console will have perfect emulation. Could be wrong though, Nintendo may go the Midway Arcade Treasures route with tons of glitches in the emulation.
I'm interested to see if they can get Star Wars: Rogue Squadron or Battle for Naboo running on the VC, as currently these two games are completely impossible to run on any PC HLE-based emulator.
Doesn't the latest version of PJ64 support them?
N64 stuff is harder and probably all you can hope for is higher resolution.
Some enthusiastic individuals have achieved texture replacements however. Polygon model replacement may be possible too?
The latter was not uncommon in the N64 era (all my N64 games do it), and it presents a problem for increasing the resolution of games. The issue is that there is nothing special about the backbuffer to let you modify adress calculation and writes to scale up the UI.
I believe the Zelda emulations on the cube had reworked UI's, some higher res elements, some stretched out elements. (like the maps)