Lots of people didn't come back at the end... Not just Mr. Eko. Also thought it was strange that Sayid didn't end up with Nadia, instead of Shannon just for starters.
They should have had something in the flash sideways make it so the flight never takes off, or what have you, and they never go to the island in the first place. Would have been happier with an ending like that. But, all in all, I only saw the finale once, and may rewatch all 6 seasons (if I ever have time) and judge it again.
Was I a little disappointed at the finale and the plotholes? Yes, to a degree, but was also satisfied with what they did give us for 6 years. Well, except for all those damn hiatus the show took...