I wanted the flash sideways to be another reality and the time lines to merge.
Explain the Dharma sharks and why the smoke monster made machine noise.

I'm with you on the flash sideways and merging. As for the shark, I believe, much like how they were doing experiments on Polar Bears to see if they could get them to successfully live in different type of habitat, the shark was something similar, hence why the Hydra station had tanks. The shark originated in there and somehow got released into the wild. As to what specifically they were doing on it, not sure.

Edit-Per Lostpedia, according to the blast door map Dharma was doing a selective breeding program for Great White Sharks. Also apparently the Dharma shark was the one swimming around the horribly CGI'ed sunken island in the premier episode this past season.

I really would have hated that ending. I guess to me that would just make the entire sideways stuff pointless if it just somehow merged with the island timeline. It would be like the Losties would be merged with happier selves in an alternate reality and yet they could never lead those lives because they were stuck on some stupid island. That ending idea just sucks.