The presence of Vores etc. in base maps is explained by the war. They are part of Quake's assault troops. You have a point though, in that mappers could make it a little more obvious that the base is under attack, and the vores and fiends could emanate from broken slipgates and so on in order to drive the point home.
And I agree about better AI for certain monsters; at least the military style enemies, despite being "mind controlled", should probably instinctively remember their squad based tactics. We have "monstergroups" already where they will alert each other and not infight, but this feature is still underused and it needs to be taken further.
Also, I personally appreciate the way it is done in Crysis, where the mapper can place AI anchors (entities) to tell a monster "hey, here is a good hiding place and please pop out of cover in that direction".
Finally, the nailgun is a lot more range ready in RMQ than it was in Quake. The nails travel faster, which increases the accuracy over range. So this is one reason why you're given the nailgun right at the start in e2m1rq.
And finally finally, like Louis hinted at,
http://spawnhost.wordpress.com/2011/12/18/protagonist/
