My Strategy Guide found here...

lol. I didn't go over difficulty spike because it is hard to quantify. Game has enough randomness that it is difficult to really say exactly how much a threat level of +1 matters. But it does make a difference. On the 4/5, I tend to use ship reinforcements from the unlockables to help.

I would focus on the hardest factions. For me that is UNKNOWN first, Trolgar, then Celestial. Removing one seems like the right thing to do, but in practice I doubt it makes that much of a difference. That enemy can no longer counterattack but another will instead.

KingAero, by the way you have private messages disabled. Check your settings if you want to receive them back.