The academy randomly bypasses my systems every now and then and bombs them. Usually they leave the system after one round, but sometimes they don't. Is that a bug or intentional? Just annoying...

This is "intentional" and happens because the Academy has a religious forced law which makes them besiege you in a cold war state. This is completely inappropriate and should be fixed as much as missing Laws and dissappearing tooltips.

For now my only advice is disabling Awakening, which doesn't bring anything worthy to the game anyways, imo. ES2 is so much better now without it.

I agree with Mamarider, disabling the whole DLC just makes the game more enjoyable and with better pacing. I got so tired of having the Academy fleet randomly killing off my outposts that I switched it off, haven't missed it for a second. Besides having features like Spear of Yssander (or however you spell it) makes factions like UC unplayable anyways, and if I have to chose between having UC or Nakilim available I'll chose UC every time