Once upon a time, a thread like this came up on this board (I know, you're shocked), and someone made a great suggestion, which I've since swiped for my own use.
Basically the problem was this: Magic Missile is a great spell, because it's simply raw damage with no drawbacks. Almost nothing can stop it, and the damage is respectable even at higher levels (3.5 per missile, up to 5 missiles per volley). Not enough to bring down the bad guy by itself, but enough to make a difference.
The suggestion was, reduce the damage but compensate in other ways. For example, drop the damage to 1d3 (average 2), just over half the old damage, but have Magic Missile act as "continuing damage" for the purposes of Concentration checks. That is, any spell cast in the next round requires a successful Concentration check with DC 10 + (half of the MM damage taken); obviously, the more missiles you use on each target the more likely you'll interrupt.
There. You still have an auto-hit unstoppable damage source for when you really need it, but the damage is low enough that it's not a good primary attack form. On the other hand, it now has a great anti-caster secondary effect that keeps the spell useful at high levels.
(If you add higher-level versions, have them do the same; a DC of 11-15 may not seem that bad, but when it gets into the 20s and 30s it gets rough).