Yeah.
The above shot is the entrance to the second indoor part.
http://spawnhost.files.wordpress.com/2011/09/e1m1rq_outside.jpg
In this shot, the bridge and the lift are to the right (the lift room is behind another of these arches). Crossing the bridge was turned into a mini-objective (without being called such) where you have to press a button to extend the bridge. Otherwise the route is the same.
There is a second entrance to the nailgun area now (to the right behind the helipad) leading through some new areas.
The base got more of an outside, but the route was changed very little.
Preach's "Beatles" comparison is apt; if Quake is "Abbey Road", RemakeQuake is a tribute album. It's not the same, because the original is untoppable. So why not have some fun.