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

[Ruinous]

You must have a repair system on any mothership. If it gets banged up set the gamespeed to x8 and wait for it to heal up before going further. Use the MIRVs, there is a reason for having missile boats in the game
I know it is tempting to save up perk points for the really big perks, but the only one you really need is the ace pilot to fly the 5th gen fighters... and even then you could probably get by quite easily without, point being get those points spent as it makes a huge difference. Oh yeh, pimp out that mothership or you really don't have a chance!