Give the AI some good waffle-beams (each output should have its own computer if server xml's allow it, which most do), they have the best target tracking amongst AI weapons by far, they'll just swap target to another block rather than fire *through* the enemy vessel.
As far as putting some logic JD's on your docked reactors, nice idea with one caveat, jump inhibitors are a thing.
Another good redundancy system is making use of magnetic docking to re-dock your free floating gens shortly after they undock, give them lots of redundancy rail dockers along the tops and sides, and add corresponding rail basics/the green & blue rail thingys.
This works against the worst of the collisions, which is when you're sitting still and the reactors just bounce around inside your ship/station instead of clipping out. This will simply reattach the generator in the same spot but on a different docker. Less effective while moving quickly or turning, but in those cases the gens usually manage to exit the ship quickly after so long as the server doesn't crash.
[DOUBLEPOST=1462070670,1462070447][/DOUBLEPOST]Another thing with Gens, if you don't want your big/high gen count battlecruisers and up to get griefed through one very annoying & exploity tactic, give your gens some shields & armor. Or the more clever & unscrupulous pirates will just bypass your fancy shields and take out all the gens safely (hint, they load quickly, bigger things they're attached to often dont...). Mostly a problem on outposts & floating ships, things you can't immediately defend.