I thought the finale was great, a HUGE departure from the norm, a great setup for some great stuff to happen. If they'd kept the whole Cylons chasing them thing up for much longer it may have gotten stale. There are now 1000 directions they can go with this wheras if they hadn't done something so drastic they were very limited.
This blows the original series away. It was so 1 dimensional with no backstory or sub-plots, this one is very intricate without being overwhelming. The characters actually have depth, including the Cylons. If you watch the finale of any show without seeing much of the rest you're bound to be lost, as the larger story arcs need to be resolved, but throughout the rest of the season there are numerous smaller plots that last for only one episode and yet tie into the whole of the story.
I like sci fi a lot, but most of it isn't very interesting or thought provoking. this series has managed to raise a lot of interesing questions about a great many things, it reminds me of ghost in the shell.