I agree that having 'push' opjects as well as 'pull' objects regarding enemy fleet movements would be interesting.
Hazard beacons to make enemies jump a few systems away from your current location, which would help greatly if you go and decide to clear the whole galaxy - clear out more open areas so you can mop them up, without enemies sneaking around you through a chokepoint - at the expense of more concentrated enemy encounters later.
False orders, making every enemy in range select a random system on the map and begin jumping to it - to scatter and thin out fleet encounters. Right now, distress beacons can only concentrate the enemy. If you have a fleet of fifteen ships looking to jump on you, all you can do is jump around hoping they split up, while the factory keeps pumping out ships.
I disagree with making the nuke cannon a drop-only weapon. It's really kinda useless to me. If you hit 100% of the time, only a few weapons match its DPS, but if you hit 50% of the time - really an optimistic estimate - many of the purchase/drop-only weapons outperform it. Ion cannons, photon torpedoes, flak cannons, vulcan, tesla coil all outperform it on DPS with no upgrades. That and the fact that upgrades are so much cheaper on other weapons relegate it to the category of novelty weapon, to me.
I agree that upgrading point defense is useless - at most, I might upgrade lasers once, so they have the hull damage to reliably take on missiles and rockets, with better accuracy than gatlings.
Projectile cannons, without refire rate upgrades, need shield damage upgrades.
Fighters still chase missiles and rockets, even if they don't go off-screen. Having to cross the entire map because your idiot ship refuses to sent drones out for a mere fighter, and your gun crews refuse to stop firing rockets, is amazingly irritating. Perhaps pop a ring up around the ship when selected, just as when you select enemies, permitting you to turn off certain weapon systems?
I would still like a 'move to this' option when selecting enemy ships - chasing a missile ship down often takes a lot of micromanagement of move orders, especially when they're faster than you.
