well you sure dont help the vis do you.
its as if you did a fast vis and not a full vis.
things are being drawn miles away from where they are.
And just about everything carves into everything else making more polys than needed. take these lights for example...

move them down by 1 unit, null the top and then the big flat roof doesnt get chopped into 4+ polys.
there are thousands of lights about that look like they were added after you made the rest of the map and therefore you have just stuck a 6 sided shape to a wall which in turn carves into the wall. even if you didnt want to imbed them in the walls you could still do like i just mentioned and move them 1 unit away and null the unseen side.
Also you windows shown here...

could be just 1 brush so its 1 poly not 4.
if you work on your brushwork it will reduce your r_speeds which i notice are a tad high in some areas....

(there are a lot of areas where it reaches 900+)
...and it will probably fix some of the vis problems.
there is something really wrong with one of the doorways as you can pass into the void one way, to contine into the next part of the map but you carnt go back (as you probably know) which suggest there is some kind of entity or brush there perhaps?
but quite frankly i would expect vis problems with a floor hacked up like this....

there are also some other things you have missed such as...

and

also the is a huge annoying bit of glass right above marine start...

and the elevator in MS starts at the top and u have to move under it to make it move down, then it comes down quick, hits you on the head and goes back up!! v.annoying.
However the funniest thing was when you join a team you get completly random times displayed. and its about the siege door not even the main door!!
heres the first complete so you can see the game time...

heres the rest....

notice the last 2 are in the ready room!! i hadent even joined any team yet.
P.S like the secret room.. hehehe
P.P.S i found around 20 problem brushes. and have screenies of them if u need to see where they are