
Maintain 4 lets you repair all your weapons, and Modify 1 allows you to upgrade several weapons (you get auto-upgrade items to improve the better weapons to upgrade two). Hack is awesome, but the stuff you need over 4 to hack is not worth it, and only appears really late anyway.
Get Hack 4, Maintain 4, Modify 1 and Research 1. Stats aren't that important, just get 4 of all except PSI (more late game if you're done with everything else) and you're golden. For Heavy Weapons, just 1, for the hilariously broken Grenade Launcher. Standard weapons rock, get it to 6 by the fourth deck or so. You can start with Hack 1 and Standard Weapons 3, two critical skills. You can try being Navy or Marine with a bit of Psi power on the side, but you're pretty much gimping yourself. Either go all out with Psi, or don't do it at all. Fine, save your game before you try to kill a protocol droid with a wrench. You're probably gonna try it anyways just to see what happens. Don't try to kill a protocol droid with a wrench. So if you come across any shotgun wielding maniacs whose shotguns always break once they die, pick up the shotgun, unload the ammo, then toss the gun. Broken shotguns still have one shell in them. There's a reason this game shows up all the time on scariest games list.
Get a good set of headphones, turn out the lights, and play at night for the first two levels or so. Generally, I like the respawn rate as it is, but the original weapon degradation rate is a bit too high, and prefer to set it at about 0.5. Although you may want to read the readme file for how to lower, or shut off weapon degradation and monster respawns. If you have the latest official version, then plain vanilla is fine.
This has to be done each time you run the program, but should let it run normally. Open SS2, then go to task manager and right click on the ss2.exe (whatever it is called), go to "Set affinity", and uncheck all but one box. The game can't run on multi-threaded CPUs.