Super Mario 64 does indeed run faster, since its not using N64 hardware, though some of the nifty effects are gone, such as the Invisible Cap Mario doesnt look like colored static as was on the original; just transparent. Try looking at the pyramid after standing on the four pillars. The debris and the explosion cause no slowdown whatsoever.
Also, maybe its just me, but the HUD graphics look less sharp than originally, also theres an emulation error at the beginning of the game. Look at the front door of the castle before walking on the bridge. You'll see Lakitu sitting at the front steps, before he 'warps' behind Mario to talk.
All in all, its the same game as was on the 64. No Luigi, no 30 extra stars, no 'game fixes'. Its the same game from 10 years ago.