Looking great so far. Yes, Q2 maps are terrible about chopping up polygons. Unfortunately that's what we're stuck with until a) I finally get my ideas for a new map format implemented (which could well be 1-2yrs worth of work), b) id releases the quake3 tools under the GPL, or c) somebody creates a q3map compiler from scratch and releases it under the GPL.
I think there are some tools released that reduce the polygon chopping, though. Another side effect of scaling textures is that it scales the lightmap as well. I'd avoid extreme values like you have with the dirt/graveldirt/gravel piles. To see why, load the map up with deathmatch 0, then type gl_showtris 1. This will let you see how bad the polygons are chopped up. Perhaps a different texture at a normal scale would be more suitable. Keep in mind that we are (slowly) working on a highres texture pack with 4x the resolution, so things will look much nicer in the future.
Also, near those dirt piles, if you jump up, you can see there's nothing there -- it looks rather weird. I'd put a ledge or something to at least give the illusion that the building is solid.
I wouldn't mess with any machinery or stuff like that. Building that stuff out of brushes always looks cheesy in my opinion and eats up wpolys like no tomorrow.
Your bases need more light -- the outer edges are either too dark to see at all, or if you crank the gamma up, you get weird colored splotches. The rest of the map is lit fairly well, but I would consider using arghrad's sun feature outside in order to make it a little less bland. Documentation is at
http://www.planetquake.com/arghrad/ . This will also fix the weird shadows along the top of the buildings.
The sides of the barrels are scaled down a little too much - the top rung should line up with the top of the barrel. Also, a couple blue barrels have the wrong texture on the top (near the piles). I like how you've made them a more realistic scale, though, rather than the 7 foot tall barrels most of us make.
Also, very slight misalignment on the top of the boxes by the blue base.
Some of the barrels/boxes are spaced far enough from the wall that it looks like there's enough room to squeeze through, but there isn't quite enough. I'd either move them closer, so they make for a defensive spot to shoot through, or move them further away so you can fit through. It's frustrating when you're in a critical situation and try to run through something but can't fit.
Another thing you might consider adding is support for multiple game modes - I think this map might work with a single flag in the middle warehouse as well.
To test your map, you can either do debug1 1, or sv addbot. set skill -1 makes the bots not shoot. If you want to test jails, you'll also need to set debug3 1 and debug4 1 and type kill.
