Someone reported that Nature Shrine and Time Shrine gained from ruins don't work (it was on pbw forum). Some AI designs keep poping into my design window, despite the fact that I marked them obsolete (Design 115 for me). Also AI keeps constructing WP with tons of minimounted Assualt Rockets. AFAIK they can installed on Fighters only, but AI dont't get bothered with such restrictions
I believe these are bugs.
Some thoughts: as we have a Tugboat hull you can implement Science and Spy Satellites with generate research and intel abilities on hull (but no weapon can be put on them

), drone and mine warheads with special types of damage, add some guns with Point-Defence weapon type which can target ships/planets/bases (flying shoting stars hehe)...
As for mine cloacking devices, well you can use your minesweapers as always, to avoid reseaching a bunch of sensors.