Yes, most of the plot was predictable, but the execution was top notch.
The 2 parter is right up there with some of my favourite Trek episodes.
I don't really see why predictable is a flaw – there's, of course, yawn predictable, but there's also what you anticipate, fear or long for to happen, among others. Surprise and mystery are not the only things you build a story out of, and the surprise was last week. This week, we were dealing with it. Not that last week's one was not predictable, it carefully sewn into the Isaac persona from season 1. Isaac has been always frightening, and only reason I stopped short of saying he's going to kill everybody is that I ship Claire/Isaac. That the signs were there made it better when you didn't see it coming, because it kicked you on the floor better, even when they literally told you the Kaylons are building megaweapons for some purpose minutes earlier. Surprises that come completely out of nowhere suck, and there's little Part II could have done that didn't fit that description.
Isaac turning on his people and seeking the help of Krill were the two things they have been building towards – with Isaac surprising discovery of his own attachment to Claire last month, and Mercer's tendency to have unrelenting optimism and unconventional decisions with his interactions with the Krill. Not going there would have felt contrived at this point.
I thoroughly enjoyed this. Outside of leaving Earth unscathed, which one may question as it subdued the dramatic potential of the battle, there's little that I'd liked more. The cliché “surprise” at the end of this one would have been a simulation, a test, or other kind of reset button – even if it was one you didn't anticipate, it would have been really disappointing. Personally I would have liked a little more in the way the discovery about the Kaylons reverberated, particularly with the Krill, or of the Krill arrival themselves, not that I didn't enjoy Admiral Halsey's reaction fully, but that's personal preference.
Besides, we only put a temporary stop on the threat, turned the set up of the whole show inside out, and are in uncharted territory. That's...
something.