The D-mods on the salvaged ships seemed especially severe (a damaged flight deck on a carrier renders it essentially useless).
Wow. You're gonna have a very tough time in 0.9 if you are that unreasonably picky.
The damaged flight deck is fine, having any fighters (even talons and broadswords) out at all is a HUGE difference in an early game "both you and the enemy have tons of d-modded crap ships" battle and can very easily swing the fight on their own, even with reduced speed and health from a damaged manufactory or with reduced replace rate from the other fighter d-mod.
2 sets of basic fighters with that d-mod debuff can still solo-kill any destroyers (or venture) in those tutorial battles (i literally just quickly re-did the entire tutorial to test this to make sure i wasn't just lucky in my past few savefiles) while you just dart around punching frigates. Heck, in the second battle I just hung back and did nothing and still won with no losses.
The other d-mods aren't a big deal, either, your opponents' ships are just as *** as yours and you outnumber them (after salvaging ships in the tutorial, your fleet is bigger than either of the two pirate fleets, and they don't seem very enthusiastic to engage 2v1).
Again, I do not understand how you can find this tutorial battle difficult. If you have to restart 6 times to "not have unacceptable losses" (which is already questionable, if you consider all the d-modded ships you're given "useless" how can any los be "unacceptable"?) I wonder how the hell you're playing the game, if I can quickly destroy those without any ship taking hull damage at all, on normal difficulty, without putting in all my skill points (to save time in this quick test run).
Those battles are extremely easy given the huge pile of advantages the game gives you to prepare for them.