After starting a new game I realized I was having a separate issue. You see after taking the first planet I went to the next planet over, and there were about 800 mkII ships (however many squads) on each mkII planet. I'm not sure why, I didn't increase AIP or spawn any waves. However, after restarting, now they only have 96 ships. So I guess yay, it's not actually that hard?
EDIT: After playing a bit, Yes, it is that hard (the extra ships were from the guardians, I forgot about that). While not impossible to take, it was much harder than necessary. This time I received enough science from my first planet to purchase one tech (that's never happened to me before). So, I decided to see just how long it would take to clear the planet without my ark. It took me over twenty minutes, and 10 full refleets before I cleared out all the ships except the immobile guardians.At that point, I sent my ark in to mop it up because I knew I would take it anyways.
I feel justified that it should not take that much to take your second system. I understand that previously there were too many MkIV, but previously you could also steamroll the first two or three near you before hitting a MkIV planet. I couldn't imagine the time it would take if you wanted to play a low AIP game with this balance, only taking planets of value.
EDIT2: I just tried using my ark, and it took three refleets plus whatever my ark produced while on the planet. While not nearly as bad, it still concerns me.
However, I've realized that I'm getting far to ahead in terms of balance, what with the fact that there are many things still to do, and as my immediate problem is solved.