I know what you mean... It is fairly hard to justify the resources to build plasma weapons in bulk.
My ships tend to be really heavily armored, at the expense of everything else, and I build a lot of radioactives extractors, since I know I'll need them... that gives me more wiggle room for installing the high energy toys.
And of course, you can't have your entire fleet be made up of plasma battleships. I had only about 15-20 of them in a fleet of 300. But despite their small numbers, they really cleaned up, scoring at least half the kills in that battle.