I hate the bonehead moves of TV execs as much as the next guy, but there actually is some logic to the programming of Lost. (And to those lamenting that shows like Lost and Firefly didn't get picked up by cable networks, the fact is it's all about the cost of production, and most network shows are greenlit with a price much higher than a cable network can manage.)
Lost is airing at a late time slot now largely because it was failing on a certain function in its earlier Wednesday slots: It was an ineffective lead-in. With many of its loyal viewers immediately going into "How about that cliffhanger?" discussions at the end of each episode (either in person, on the phone, or online), and the heavy "active viewing" component, fans were generally not in the mood to get hooked on other "active viewing" serialized fare like Invasion or The Nine, so ABC eventually set Lost up as a night's grand finale.
And the "on one week, off the next" argument is an old, outdated one (that I never fully cared to get into). The network season structure has long been "New episodes in September and during the three sweeps months, with reruns peppered in between," but between the serialized nature of this show and the habit many of its viewers developed watching all-in-a-row cable series, Lost fans acted like the standard network model was an affront through the first two seasons. The network tried a compromise in the third, splitting the seasons into a short and a long "pod" so that it could launch at season's opening in the fall and have episodes during November sweeps, then disappear and have an uninterrupted run from February sweeps through May sweeps. But people didn't like that (the six-hour fall pod was a turn-off to nearly everyone), so they tweaked again: shorter seasons, springtime only, from February through May.
And had there been no writers' strike, the show would have run for sixteen weeks, uninterrupted. A five-week break was taken in March and April only due to the strike, and the two-week break between the penultimate and final episodes of the season was done solely to account for two-hour finales of both Lost and Grey's Anatomy, a collision that might have been avoided had the timing worked out differently without the strike.
I know it's popular to complain about the networks (and I've done plenty of it myself, in relation to several beloved shows), but ABC seems to have done the best they can to adapt the scheduling of this unusual program to the audience and production circumstances they're faced with. That, combined with making the "48 more episodes over three seasons" deal last year, makes them better execs than most in my book.