Well it's no surprise I hate where this lead to. Commander (not Admiral) Cain was a god-like tactical genius who had the loyalty of his troops cause he was the best warrior of his age. Instead we now have a total hatchet job turning HER into a totally psychotic, power mad biatch, with no morals what so ever. I love how she initially had Adama's same attitude about the President, but then totally ignores her and does her own thing thereby unvalidating the Colonial government (Um, the people SHE supposedly takes orders from?)
My biggest gripe is that Roslin could have taken a stand right away and asserted herself as CIC. First instance of Cain getting out of line would have been a repeat of the earlier revolt. This time the civillian fleet AND the galactica would be against the "renegades" of the Pegasus.
A better begining would be like this:
Cain "Welcome back to the Colonial Fleet"
Roslin "Actually Admiral, that's MY line."

As for the new Cylon ship... I bet Baltar IS a Cylon, that is his command ship. Baltar is the Imperious Leader... Just my guess.
In the Original, a demonic entity (Count Iblis, Satanish, The Devil) was the Imnperious Leader for 1000 years and tricked Baltar into serving the Cylons.) I would be VERY interested in WHO the new Cylon God (or what) turns out to be...
I would like to see the return of the Ship of light and the "angels".