1) Thanks!
2) Yeah, I'm thinking that the final points could be spytech bases behind the mills. That, or somewhere in the terrain between the rivers and watermills could be the outer points and the watermills house the final ones. I think I don't want the points to be as close to one another as Valve would do, though. I think I want them to be a bit further apart and take longer to cap, so instead of it being like "yay, we're at their final p- some scout's capping our point", things would play out much more slowly and control of the points wouldn't fluctuate between the two teams as much. This may change, though.
3) The grey pathways are tunnels. Do you mean the background color, the pale lime greenish thing? They can't, with one exception (oversight on my part). If you didn't know, the brighter green areas are higher than the darker areas. I fixed it - the whole region between the higher areas and the river would be accessible, I may put the secondary spawnrooms down there or something. The area circled in red is technically an archway that runs above the lower ground.
4) Good idea. There's one thing though, I don't know if I want the rivers to be fully traversible as that may make the map too open. A fall from the bridges over the rivers (the bridges in the center, not the mill bridges) should kill the player (hey, it's a shallow river). I may fence some areas. Not sure yet.
5) Thanks!

*again*