The brief cutcenes with Quiet later on are most enjoyable, actually more like the older MGS. Such a shame they cut back on the story so much.
If u rescued the ppl u get them in ur base u also get the sv sneak suit, cheaper than the other sneak suit but doesn't have upgrades
I tend to kill / extract all the guards in these places so I can loot everything in the base without being bothered. I was scared of those nasty jumpy glowing eyes chaps from the time where I didn't have my horse against them so I legged it and just as I was leaving the area it told me to use it on them. I went back but they were gone. I then used the honey bee on some random crap and realised how kick ass it was!
I tend to tranq people so that I don't have to worry about them if I'm seen. Its just super hard to take anyone when there are so many people patrolling in a small area.