I can see where anyone who is anti-religion is going to hate the ending, but it is a fantasy show, so get over it.
I thought it was great, the whole shebang. I really liked the way they didn't end it totally. You've got Ben and Hurly running the island, you've got a bunch of folks making it back home. The ones who didn't make it found each other in the alternate reality.
I teared up three times. Jin and Sun of course got me, that was the best romance. Charlie and Claire also got me, which I was surprised by given my meh-ness towards Charlie. Sawyer and Juliet was pretty great too.