I don't really expect MM to ever balance the weapons. I think they have many, many more pressing issues. For example, didn't I see that they are just now beta-testing a fix that will let the AI use troops or somesuch?
I think it is up to the modders out there to sit down and completely re-design the tech tree. I think everyone agrees that it has even more gaping holes in it than the AI.
But while it is a lot of fun to design your own races, re-designing the tech tree is a pretty daunting task.
I have an idea for a program that will let you compare the ships of different races at particular points in time so that you can evaluate what changes to the research order and ship designs will have vs. another AI.
The biggest problem with completely re-designing the tech tree is going back in an play-balancing everything. If it were possible to make one change to a weapon and then "predict" its effect on several different races, then this task would be much, much easier.
Writing such a tool would be a lot of fun--but not more fun than sleeping.
BTW, whose idea to allow 100 ships instead of 30?!?