I don't have any experience with crashes in Project64 compared to 1964. Just about every frickin' game (though very rarely).
As for speed, I think it should just all be evened out. I mean, I'm just saying the way I think this works. I think it's more like, the more game support is implemented into Project64, the more decrease in general speed. Maybe take some speed out of the relatively fast games and put a little of it in some slower but fairly popular games. That's basic, but about all I can say. I don't know much about how speed works.
Oh, but there is this. Sometimes, when I exit Project64 without directly closing the ROM first, I get a Dr. Watson's error message, Project64.exe has encountered a problem and needs to close. We are sorry for the inconvinience. I've never heard of that happening to anyone else, so I think it's the registry, as when I first installed Project64, it was unable to write to some parts of the registry (since I have a limited account...I hate Windows XP for that).
But for those who do get crashes in Project64, speed isn't as important as the prevention of crashes in the games, unless a major sacrifice of speed is involved. But there are PCs out there that can emulate at high speed to counter games with slow speed, but not control the likeliness of a game crash. So I would have to say the prevention of crashes is a fair deal more important.