Well I'm a big fan of Cryptics CoX (currently play it), and I've been following Champions for a while now and so far the ETA on that game is Spring '09. With that said I would bring this up:
-If it is Cryptic you won't see STO untill post Spring '09, as I mentioned before Cryptic just dosn't have the resources to pull off multipul MMOs at once, the facts are there MMOs take the most resources and the most manpower so with that said I doubt you're going to see a Cryptic spin on STO for some time. Heck to make maters worse they seem to have a second IP in the works (judging from the art on their page), and the fact that they are showing it off screams that they intend to prasue it asap... or to put it plainly after Champions is finnished.
-If it isn't Cryptic than its obviously someone smaller, as no one can come up with another bay area dev that works on MMOs. I would like to point out though that it could be yet another new studio, possibly someone backed by a large company... possibly Paramount/CBS. On the otherhand who is to say that they are actualy in the bay area, I know this sounds shady but no one said that PE had to announce the truth especialy when they were a sinking ship, they may have been throwing the new dev a bone keeping us off their trail by focusing our view on the bay area. This is however an unlikely senerio but not impossible.
So far the evidence dosn't point very strongly in Cryptics direction (at least in my opinion). From what I've heard people talk about, the only info most people are going off of is that Cryptic is in the bay area, and that one of their high mucky-mucks was wearing a Trek shirt. I'm sure there is a ton of evidence people have fished up, but even companies like SOE have drifted away from multi-mmo development. Currently their only project is The Agency. The modern trend it seems is, develop game A. As soon as game A begins to finnish up beta start development slowly on game B, but take the time to continue to update game A to ensure it lasts more than a year. This leads to game B having a long development period. Who can do this? Well only NCsoft, and SOE come to mind and both companies have their own IPs that they are working on, The Agency and Aion. Cryptic just sealed a deal with HeroGames to do Champions, all of these major companies are currently busy with other announced projects and with a slacking American economy I doubt anyone of them wants to take a risk on taking to big a bite of the pie.
So with all that laid out for you to see, my conclution, Cryptic... iffy and doubtful (but hopeful... though if they have it I'm sure it'll be a long time till we see the game due to Champions' current status as top on their list... heck they are even aiming for a multi-platfrom launch again high development costs and tons of risk). The chances that some tucked away company that dosn't want attention at the moment... more likely (hopefuly they are a crew of veteran MMO devs, you never know with our saging economy people lose jobs and then they ban together to build a company when there back is to the wall). Hopefuly whoever has STO is giving it there full attention, which is somthing I would worry about if Cryptic had STO... they've got a baby on the way and another one in the oven so they have there hands full, because it dosn't end with launch.