I just want to get this out now so I can say “I told you so.” Since it involves spoilers, only continue below the fold if you’ve seen the season premiere of Battlestar (or don’t care about having it spoiled).
Ellen Tigh is not the “last” cylon. She’s just an aged version of Tricia Helfer’s “Six” model cylon. The tells are physical resemblance (compare Helfer and Kate Vernon, who plays Tigh) and their hypersexualized seductress personalities. The real last cylon will be revealed as Anastasia “Dee” Dualla, who shot herself at the end of the episode (uploading her consciousness back to a cylon resurrection ship point). The body in Kara Thrace’s crashed ship will turn out to be a Dee model—note the ring on her neck matches the one Dee places in her locker before shooting herself. (I should add I’m much less confident about this last bit.)
Update: I missed a few data points—the most obvious being the way Saul Tigh used to keep seeing Six morph into Ellen, suggesting some sort of link there. Also, note that Dee—one of the few characters based on someone from the original series to get her name changed in the process—is named “Anastasia,” from the Greek for “resurrection.” (The Six hiding on Pegasus chose a last name, “Inviere,” that means the same thing.)
Some problems with those theories raised in comments: Didn’t they destroy the cylon resurrection hub? I can think of a couple possibilities here, but the easy one is that if the humanoid cylons—or at least the Final Five—originate from Earth, it stands to reason that there might be a resurrection point on the planet somewhere. That might also explain Three’s decision to remain on the wasted planet.
The other problem, of course, is that Adama and Tigh have known Ellen for years—wouldn’t they have immediately recognized Six as her younger self? Tigh, who would be most intimately familiar with her, isn’t that big a problem, since it’s well established that cylons are often programmed with memory blocks designed to prevent them from realizing what they are. Indeed, his visions of the captured Six as Ellen could be a side effect of some sort of block that causes him to remember Ellen as always having appeared as she does now. Alternatively, and more generally, this gives us plenty of reasons to be skeptical of the accuracy of Saul’s flashback.
Adama is a little trickier, but maybe not entirely impossible to explain. The most familiar appearance of Six is the Capirca/Baltar’s Head version with platinum blonde hair. Now compare her with the Gina Inviere Six and Natalie Six. They’re all Tricia Helfer, of course, but they look pretty startlingly different. That may leave room enough for variation that Adama wouldn’t necessarily recognize the Ellen Tigh of a decade ago as a version of the Sixes he’s seen.
Update II: I may as well tack this on here, but with pretty clear evidence now that the humanoid Cylons long predate the Human/Cylon Wars that occurred some 60 years ago in continuity, I’ll bet that the 12 models of Cylon correspond to the human gods. We have—somewhat conspicuously—never actually been given a number for or exhaustive list of the human gods, but at least 10 have been named, and there were 12 Olympian gods in Greek myth, most of them sharing names with the human gods who’ve been identified.