Later in the game you'll get a couple weapon options that make the choices a bit easier. I tend to carry two automatic rifles; if I run out of ammo in a heated firefight it takes less time to switch to the second weapon than it does to reload the first one. Oh, and reload constantly. If I fire even just three shots from a 30-round mag, I reload. Not realistic in the least, but neither is the enemies' near super-human eyesight.

Been a while since I played, but if memory serves the shotgun is also good against the heavily armored guys - strips that armor protection away a bit quicker.

Edit: some weapons also have a secondary fire mode that can help with your decisions on what to carry.