I tend to leave doors opened when there are some supplies inside room.
If everything is used, it would be wise to close them, thats for sure.
Shotguns are not useless - they kill everything except Elites (thats what Krak and Inc grenades are for) and Workers (outrunnable, can be ignored to some extent, and not worthy to be attacked). It is not wise to waste Smartgun ammo on 10 hunters/warriors when you can use shotty, is it?
Using medikits depends on your Medical skill level, being radiated/or not, etc.
Escape route - I make screenshots with the position of lifts, so yeah thats the same.
Firepower / armor - you are generally right, but ...I died few times because of hunters' run and attack speed.
With some armor I could outlive it.
In other words it is pretty well balanced, imho.