I don't like your stage 2. Here's why:
The first thing I notice is I'm rendering your whole map at once.
From this spot I can see 2 of the 3 paths from the intel to the point (the one I can't see is the other spawn area). I can also watch the point area a little. That's a lot of visibility, and it being arena only makes it profoundly worse. Not to mention it's all death pit everywhere around it. By the way, I'm a few feet down one of the paths here, and I can only just start to read the signs. I need more indication of where I'm going before I dedicate myself to the route, especially when they're so visibly different.
Your lower area is kind of completely useless. I kept expecting something to be back here, somewhere, but I was killed before I was able to explore it every time because the teams meet so quickly. It was 4v4 or something so who knows, but I think I'd still have expected something to be here on a full server. I just don't know why it exists if not.
I actually don't know why the lower area exists as it does... it's so disconnected from the rest of the map and strategically worthless to boot. I kept thinking the flag spawned down there, for a few reasons. The first reason is you only have one sign on the lower area and it points here:
I kept dying when I got here, too, so I didn't know this was wrong for a while. But the interesting geometry and the fact that I knew the control point was above and behind me made me think the flag was behind that pillar, or that the pillar would descend and the flag would be there. Also, the HUD arrow actually points right to that pillar because there's no way for the arrow to show players if the flag is above or below them--so I didn't have any indication that the flag wasn't right there!
The main reason, though, is that this whole lower area is so remote and useless that I was assuming you had made it important by putting the flag down here too, but you didn't. It's just a big empty platform and stairs to the flag.
The stairs seem like a miserable flank, especially when defenders have a medium health and ammo (in arena! with respawns!) right there to help them camp. They can watch you come in and you won't be able to get close to them for a long time. I'm not sure if that beats attacking the flag room from the cap room, which looks really easily spammed out and only has the single, open, uphill, coverless route there.
This whole lower half of your map... it's not useless, but only because it's providing overflow routes for players. As a play area, with nothing of value in it, it probably shouldn't be this big or you should make it more useful.
I'd say just put stairs to the cap room there. Maybe raise it all a bit so your stairs can be shorter and getting between the two levels doesn't feel so arduous. I think you should put either the flag or the cap on the bottom floor, and they should probably be diagonally across from each other (viewed from the side) with routes of similar distance to the point. Bend the mountain paths from a C shape into a V shape so players can only snipe the bridges from the corner bend (if at all), preferably near where the point building is, and not all the way from spawn. That's going to help your VVIS issues also. And please use team colored dev textures. If you don't like the walls of red and blue, just put some stripes in.
None of this is about gameplay. It's just observations on flow, map readability, etc. Hopefully I can give you some gameplay feedback shortly.