3 years would made things too easy. I'm at 3rd year right now and only month away from unlocking gauss weapons, days away from getting savior suits, already have bio suit, guardian armor, tanks, whole 1 (one) syn, variety of laser weapons, simple hellerium explosives, 4 bases, no problem with money (even if I run out, I can just sell some of my spare parts, which worth millions), etc. etc.
Skipping some missions is ok, but you shouldn't slack off too much when you just start, or you'll be in a pickle. Even as you start, you need to gather as much as you can, so you could expand as fast as possible, and on (captain) jack sparrow, you can't afford to take your time.
Slaves are bad as fighters, but they're cheap, and bad fighters > no fighters. Just give them something like military shotguns and panzerfausts, and pray they won't hit each other.
16 gals is really not a lot people, I think I had more at year 1, since somebody had to replace the wounded. Maybe you should consider expanding your forces. And why are you still using heavy shotguns? They can't penetrate armor at all.