This game spits you in the face and the nkicks you in the nuts

[Nanaki]

Here is what my mothership has....

2x Falconet Major Calibre Guns
4x Rage Turrets (thinking about replacing with particle accellerators... they are only slightly weaker than lasers but they do not have the massive disadvantage of being weak to antilaser system equipped ships, which are freaking everywhere)
1x Tungsten Repair System (This is extremely important, as your mothership cannot repair itself without it)
1x Kali Shield System
1x Smog Antimissile System
1x Emerald Antilaser system

With a Systems MK3 AI piloting my Mothership, the Systems MK3 AI is very important, as it increases hull repair and shield recovery by a whopping 250%... that means it turns my 10 HP/sec Tungsten system into a 25 HP/sec... It also makes your mothership near-immune to the alien missiles as they simply cannot get past your antimissile system

This is my Lion Cruiser, though, my Astarte had all of the same minus the Emerald Antilaser system and minus one Rage turret... and it was able to tank aliens indefinately.