The main problem I have with nukes is that their fire rate cannot be mitigated well, and more than one of them usually just target the same ship at the same time. Maybe with manual control . . .
I usually employ no more than one energy cannon, and try to upgrade both reload and range on that single weapon. Everything else is projectile cannons with reload, bolter fighters with maxxed ship count if I have bays available. I don't bother with light weaponry (gatlings, etc) at all until I've filled out my formation and have no more heavy weapons to buy.
My bottleneck in upgrades is usually upgrade modules, but if I've filled out the upgrades mentioned above, I'll generally start dropping damage upgrades onto weapons that permit them - they're reliable upgrades in that they always improve a single stat without reducing others, so they neither cripple a weapon, nor undo the benefit of the otherwise powerful upgrades I've invested in.
