Putting it up against NCIS might be a vote of confidence. After all, ABC has to put something up against that show. Why not use a show that appeals to non-NCIS watchers? How much overlap is there between sci fi fans (and, crucially, the sci fi-liking general public - a much bigger audience of the sort that made Trek XI a big mainstream hit) anyway? All that NCIS/CSI/blah blah stuff has no appeal for me. NCIS got 15M-18M viewers over the past season. Out of a population of 300M, there are still a whole lot of people not watching that show.
I like your idea of moving it behind Lost. ABC might actually have me watching one of their shows that comes on after Lost if they were to do that.
That might be good for V, but ABC might think V is strong enough not to need the lead-in timeslot, which they would prefer to use for a less-buzzed-about show that needs the boost. ABC has to think about its whole schedule, not just one show.