The first 2 seasons were great because the writers spent a great deal of time creating this intricate mystery and subplot. But that's how all JJ Abrams TV shows start off.
But then at some point, you have to start answering some questions or else people will either lose interest because of boredom or of frustation.
I think that's what happened with Alias. When JJ Abrams left the show to work on other projects, the writers didn't do a good job of creating a great answer to the mystery. Instead it just dragged on which ultimately hurt the show. Luckily Abrams AND ABC realized this before it was too late and decided to cancel the show but not before giving ample time to wrap things up in some logical fashion.
LOST suffered from this too I think, but Abrams learned his lesson. That's why they've already annouced that LOST will only last up to 5 seasons I think and more importantly, Abrams and the crew already have the ending in the mind.