I'm not sure whats "unbalanced" really. The three types each have their advantages at different points in the game. Missles are, however better in almost all cases. Not to say its unbalancing, just different, especially if the AI goes for missles. I used to see the AI always goping the missle route and on very high difficulties you can't count on them all using the same.
If you are evil, the special evil beam weapon is quite superior until you get near the end of the weapons trees. The are also a different number of techs to get to the end wich can be good or bad. More to get is bad, but you get more upgrades faster.
Also you may have to look at the corresponding defences. If missles are the best weapon, it may be (and i never checked) that missle defences are also powerful. Mass drivers may stink, but if armor techs are also hard to get etc. then the weapon type isnt so bad. I like when the AI goes for missles since it gives me the excuss to get Aeron Missle defence which has a trade good associated with it. BTW I like that the trade good has nothing to do with defences but gives a reserach bonus.
Maybe someone will do a study...
Hey wouldn't it be cool when you research to the end of all three weapons tress there would be one weapons that is part of all of them, like a super weapon. It would have to be late in the game before you had all ofthose techs.