Honestly, rather than burst replacing refire rate as the main upgrade, I'd rather see refire scaled back on both energy cannon and projectile cannon. Either lower the numbers, or bring in other drawbacks. Just as the penalties of burst make it a counterproductive choice, the benefit of refire rate make it an obvious choice. It's not a strategic choice, because it's a correct decision - same problem in reverse.
My ideal would be for all upgrades to be more or less equally viable, balanced as well as possible. You could take burst, slowing your rate of fire and accepting other penalties for withering volley-fire, or you could take refire rate, and maintain a stream of fire. But my opinion is that development should attempt to make neither option superior. Each should be viable, and players can use any upgrade strategy, viably, to suit their play style.
Some exceptions are permissible - hull damage upgrades should be more potent than shield damage upgrades, on anti-hull weapons. Other times, a weapon will be suited to a certain play style that limits the use of other upgrades - range upgrades on inaccurate weapons, for instance. These things are a natural result of game mechanics, though, and the player is gaining benefit from his upgrades, even if the mechanics don't reward him as well for it, in certain cases. It's not a result of a development choice to make an upgrade weak, but teh result of the weapon's function.
I think the escalation of cost already severely hampers minmaxing single weapons, powerfully encouraging upgrading many weapons instead of one at a time. I think fully upgrading even heavy guns alone is a feat that only the severely dedicated player will seriously consider, let alone achieve.
P.S. - forgive me if I'm harping on and on. I'm getting sick, and my thought processes are a little jumbled right now. I'm not sure right now if the horse I'm kicking is already dead or not.
