@syneris: Ok so that makes the dual doomray option a no-go in my opinion, however, I do see a way a branched tech tree could be accomplished with relative ease. Each branch has to diverge and then go it's seperate way and end with its own unique tech. In my running example the subspace blaster and annihilator could be moved to one branch of the tree and modded to be the top tech while the doom ray's research costs could be modified to offset the change in the other branch. Let's say that at plasma III, one can decide to go with phasors or continue down the plasma route. The two weapon types can be differentiated by making plasma weigh more, do more damage, and cost more than same level phasors, or vice versa. For example, use "Plasma V" that is a size 7, sizemod 4, damage 4, and costs 70; or Phasors III which is size 5, sizemod 4, damage 3, cost 40. Depends on which path you go down. One ends in a doom ray, the other ends in a comparably modded subspace annihilator.
That's my idea, anyway. I'm going to try it right after I finish the current galaxy I'm playing.