It might be because I'm a lifer. But I think the reason that I prefer STO is because it's different. SWTOR has the same battle mechanics that almost every other MMO before it has had. But STO is different. You really have two 'characters': Your captain and your ship. Even with a single captain you can customize your abilities by switching out ships and ground/space BOffs.
While I still have a few issues with STO (I find some of the tooltips to still be a bit too vague) I still have more fun playing this than another MMO. Space combat is more than hitting hotkeys, it required tactics involving shield management, maneuvering, and speed. Ground combat is more than (or at least different from) the cookie cutter tank/dps/healer builds you see everywhere else.
Everyone has different likes and dislikes. No one game is perfect for everyone. If it were we'd all only be playing WoW. The reason there are hundreds of different MMOs is so that everyone can find the game that's perfect for them. I subscribe to 8 MMOs and play several more FTP game - and constantly go back and retry games I've left in the past to see how they've changed. It's not about whether X is better then Y. It's simply about finding the best fit for yourself.
I've taken breaks from STO and I'm sure I'll be taking breaks from SWTOR, just as I have WoW and many other games. Most of my current time is now testing GW2. They're all good in their own way.
I've been with Cryptic since City of Heroes. So it's easy for me to say with confidence that their gameplay system, i.e. combat, are usually very fun and usually quite different than the other MMO's out there.
However, after playing some SWTOR and after getting two STO characters to VA1, I have to say that while SWTOR has inferior space combat, most everything else in SWTOR feels superior to STO especially the more players are in your group. That's how things feel to me at least.
That said, I'll be back in STO whenever there's new content to experience, and I mean story-based questing, not new l00t items or special events that promote new l00t items.
Without getting flameworthy I think they're very *different* games.
Now my preference goes to Star Trek Online, simply because I'm not a huge fan of Star Wars, but I think it's fair to say that STO has an excellent Space/Ground concept that no other MMO did at the time, and is quite revolutionary for that. I know EVE did space, I know there might be better ground out there, but AFAIK there's no other real mix out there until recently.
SWTOR on the other hand seems (from what I've seen) to handle story very well indeed, but has perhaps, less than creative gameplay elements. I don't know, I didn't get far before I grew bored.
ALl that said, so long as people play what they like it doesn't really matter I guess!
People like to talk about heavy handed moderation here... but this whole Ilum thing on TOR has turned me off the game. I got a 15 day ban and character deletion for buying cheap items, which turned out to have been collected in a level 50 zone by level 45 characters, hundreds of whom have gotten permanent bans for doing so.
Honestly, right now that's what separates the games for me. STO has deleted forum threads I don't think ever should have, TOR has by their own statement banned hundreds of players, temporarily or permanently, and deleted thousands of characters, because of a design mistake that a dozen other MMOs already ran into and dealt with in more palatable ways.