3. Minimal downtime
When you die in WoW's Battlegrounds, it could easily be several minutes before you're back in the action. Some of the Battleground strategy is even predicated on making death incredibly inconvenient for opposing players, so that's not a surprise.
But even in the games where inconvenient death isn't a specific factor, like Warsong Gulch, it takes a long time to get back into the action. Heck, you even mount up in the BGs to get back to fighting. You have to mount to get to the fight.
Not so in Warzones. You die, you instantly rez in a holding pit. Not quite the same as being in the fight, but at least you can buff before you get out of the gate. (Waiting to rez and then buff, as you do in WoW, further delays your time before the fight.) As soon as that holding pit opens up, you run to the fight. Running to the fight (or, I guess, your defense spot) takes like 10 seconds. You can barely finish buffing in WoW in that time.
This constant action in SW:TOR's PvP is perhaps its single greatest strength. When you're fighting in PvP, you are actively fighting. Not waiting as a dead ghost, not buffing, not mounting, not running across a huge open field. You're actually playing the game, actively engaging and moving.
This design aspect is a huge success for Warzone PvP, and it's one I hope we see mirrored in Mists of Pandaria.
2. Rewarding objectives
One of the SW:TOR Warzones is essentially Arathi Basin. Instead of accruing nebulous points, though, you're counting down to zero. Every base (cannon) you capture means the enemy points (armor) counts down faster. Get it? It's Arathi Basin, except cannons instead of Stables and armor instead of points. It's Arathi Basin.
Something bizarre happens in this Warzone. People get yelled at to get the hell off defense and go fight. Let me say that again: You sometimes have to get people to stop defending! I know, right? Why? Why does this happen?
SW:TOR has a medal system. Under the hood, you accrue invisible points for damage, healing, and being near defense targets. Accrue enough points, you get a medal. You get bonuses at the end of the match for having medals.
While WoW has tried to give defenders bonuses, it's never quite managed the trick. However, I really like this system of under-the-hood points that grant bonus honor to players at the end of Battleground. It encourages people to focus on objectives instead of HKs. (Did I mention there are no honor kills in SW:TOR? At least, none that I've seen yet.)
1. Smaller scale
Warzones in SW:TOR have 16 players, eight people on each team. We've already discussed that the Warzones are much smaller in scale than the Battlegrounds; you can reasonably run the entire distance on foot within a short period of time.
This smaller scale translates into a much more personal experience than the huge zergs of the Battlegrounds. Your personal performance plays a very direct role in your team's success. While you could argue that 5-man Arena matches are similar in WoW, those encounters are just last-man-standing PvP matches. They don't have diverse objectives and the same kind of dynamic game goals.
The smaller teams make a difference. You get to know your team members as well as your opponents. The names are familiar, especially since SW:TOR doesn't have cross-server matching. It's a much more personal kind of PvP, and it's one that helps build community. So my hat's off to SW:TOR for that aspect as well.
For that matter, the lack of enforced premade teams (via arena or ranked battlegrounds) forces the SW:TOR community to actually play with each other. Sure, you can queue as a group, but that's not the same as a separate, rostered fish bowl. The difference is obvious when you come back out of a Warzone and chat up your servermates. That power should not be underestimated.
I don't think you can blithely say whether PvP is better in one game or the other. But you can compare the two and come to rational reasons for having a preference. My personal jury's still out, but contrasting the games has been interesting.