Yes, there was framerate issues in Perfect Dark, but it was still fun. Does it hold up? I would rather pull out my Nintendo 64 and play Perfect Dark than some of the modern day shooters...even the multiplayer.
I liked the feel of the multiplayer mode, the controls, and aiming...and I didn't care about the frame rate issues, which could be improved, by limiting the number of bots, or playing with only friends.
As for Super Metroid, when that hit virtual console I immediately played through and beat the entire game...which I had never done on the SNES. I was blown away by the level design and mood and atmosphere in the 2D game design. Things that are sometimes not even done in this generation of games that really made you feel like you were in a living world. The same is special...and is one of the best games ever created.