I didn't know it until checking right now (I've been meaning to have a good look into exactly what makes a difference for a while) but yes the N96 does have AGPS.
But...
I've been using the phone in "Offline" (disconnected from operator network/data connection) mode to save battery - this means that I lose the "Assisted" part (which relies on a phone signal) and have just been running on standard GPS. I was finding that in areas of no phone signal having the phone "Online" meant it killed the battery quickly by always trying to obtain a phone signal. I thought that since the GPS doesn't rely on a phone signal I may as well always run Offline - which works fine in times of good standard GPS connection, but for times of a bad GPS connection but a good phone signal then AGPS would make a difference. I'd imagine AGPS brings benefits even if you have a good standard GPS signal. Don't get me wrong, most of the time I DO have a good position just by using standard GPS. It's just the amount of times it goes haywire is still unacceptable. Damn technology
I'm going to try running my phone Online next time - and assuming I have a phone signal, in theory I should get a much more accurate position and track recorded which will prove AGPS makes a difference. Problem with my battery though will be if I have no signal it'll die very quickly (still give me 3-4 hours though and I have a charging unit I carry).
Waypoints - I tried them the first time I used it and got annoyed by the thing buzzing and beeping all the time. Since then I've only ever opted to "view" a route on the screen and compare that with the track being recorded over it, instead of "following" it waypoint by waypoint. But I can see using the waypoints in a lot of cases would be very useful and I'll try them again.