Truform support worked in some cases, and gave some really odd results in others. GLquake was really funky using any level of tesselation -- I think that the coders tried tesselating absolutely any geometry, both for models and the actual map making for some pretty distorted visuals. Truform was perfectly integrated into Q3 engine games like Wolfenstein, however. I think it's pretty easy to differentiate between world and model geometry, as it's been done with most games that were patched for truform support. While I'm pretty sure we won't see any of this, it would be more than doable. Ultra-smooth characters running around ultra-blocky worlds look just as unconvincing as blocky characters in a blocky world.
Adding per-pixel lighting would require some pretty serious engine modifications and optimizations and would be pretty damn unlikely. Better framerates or higher resolution for N64 games would be most likely, if the GC releases of OOT and MM are any indication.
I think that nunchaku/remote support would be pretty cool for most 1st person GC games. True, some of the boss fights in MP/MP2 would be spoiled by the free-aiming, but I think that it would work out for the better overall. It would certainly work much better in a game like Timesplitters, Geist, or any of those tedious WWII shooters.
I think support for solo remote control could be fantastic for RE4. Draw a weapon with A, and the trigger becomes the new "action" button. Timed-button pressing sequences have the graphics modified accordingly. If they mapped the analog stick to corresponding movements, you could tilt forwards to advance (steeper tilts = run, shallow or moderate tilts = walk). Aim the controller left or right to turn. Tilt the controller up to backpedal, and a quick filck does a 180. Aiming would work fine with this setup. The only issue I can think of is how to draw the knife...
Of course, I'm sure they'd save such a scheme for future RE title (or ANOTHER remake).