Sigh. I don't know what you should do, but I'm certain the changes you made haven't really helped.
To be honest, I liked 1-2 the way it was. It needed work, but it could have done pretty well the way it way. Right now 1-2 feels like an out of place section of buildings in what should be a mostly nature area of the map (I can see it turning industrial on stage 3, eh?).
If you reverted back to the old 1-2, you could move the CP up on to the middle height and make the lowest path a flank. I really did love the flavour of the old 1-2. The best part for me was always the junction below 1-1 of the two doorways at a 90 degree angle and the constant battle of flanks for a team stuck trying to push there. Those buildings now see NO use because they're so close to 1-1 and there's an incredibly easy to defend (READ: SPAM) CP much closer to spawn. It feels like wasted space now.
As for the 2nd stage, I think it's only improving. My only complaint right now is the spawn times issue, which I believe you're correcting.