Comparing the damage dealing of magic missile to other first level spells is not getting to the point. The point is, magic missile has several features that make it far superior to other 1st level spells, especially as you advance in levels.
How many 18th level wizards have you seen cast a burning hands spell? In 99% of the campaigns out there, the high level wizard would be embarassed to cast a burning hands spell as anything other than a joke. His foes will have a relatively easy time making the saving throw and the damage will be pathetic, regardless of how many targets are hit.
That same 18th level wizard likely still keeps magic missiles in his arsenal. Their advantages far outshine the other 1st level combat spells at this point. The magic missiles are hard to resist. They deal a decent amount of damage (not a lot, but as much as the party's fighter probably does on a single sword strike), they *never miss* and they deal a type of damage that nothing resists.
The people designing 3.0 knew this spell was out of balance, but the backlash to any significant changes was so large that they decided to leave it in the game in basically the same form as 3.0. They talked about this in interviews.
The spell has multiple features that verge on broken (always hits, hard to resist). The spell can't be balanced if it deals damage anywhere close to what other 1st level spells can deliver and has these incredible features.
That being said, the 'broken' nature of the spell was taken into consideration when balancing the wizard and sorcerer classes. It was assumed that the wizard would have a few magic missiles to toss out in comba when their other spells ran low ... a sort of default attack that still was useful. If you change the spell, you need to remember that this tweaks spellcasters down in balance issues.