I'm still pretty new so my opinion is from a newbies perspective (well mine anyway).
I actually like all 3:
Warp was the easiest one (as intended I suppose) and the cool down didn't seem so bad, but that may be because I play on "fast" game speed until I get into combat then I slow it down. Although looking at the spiral arm next to me with a hostile empire that was rated as "pathetic" and knowing I would never get there until I was able to unlock warp II or III was a bit annoying.
Wormholes I had mixed feelings about. It was nice starting a new game and having my 3 corvettes jump into and out of every system in range in a pretty short amount of time so I could see where to send my science ships (the corvettes were just locating planets for my science ships to scan). Making the wormhole stations was pretty painless. I did notice the jumps taking longer and longer to spool up as my fleet got bigger and was wondering how long it'd take to jump when I had a fleet in the hundreds. I never got the chance to find out though as an empire crushed me pretty early on.
Hyper Drives I hated at first. I didn't seem to jump any faster than using warp (it's possible I didn't pay enough attention to how long war takes), I was restricted on where I could go. I had some enemies (some pirate faction/empire) that had about 20k fleet strength near my starting area that made my trip even longer. I also ran into some other empires that closed off borders, so even though I could see nearby systems I could not just warp to them. But then I started a game and made everyone have to use hyper lanes only. I wanted a game where I could create choke points and such. I got lucky and ended up with a nice area on the edge of the map with only one way in, which I am using as my staging area now. And looking at the map, there are two systems that when I gain control of them I will have about 20 or so systems blocked off for myself. I am a bit worried about what will happen if the AI gets the jump drive thing I've read about (can the AI unlock the jump drive?), but I'll figure that out when/if it happens.