About the sentries at the second point: we had 2 engineers constantly fixing each other's stuff and upgrading things really quickly, so that might be why it seemed a bit overpowered to some. If you improved visibility into the area (via windows) then some of the good engineer spots on the map would be gone. Something I see far too often is "engineers are getting kills, we gotta remove that spot entirely or increase visibility into the area". When one of us had died, it was very easy for BLU to push into the area and destroy our stuff.
Something that every map needs is a dead-end area where it is easy to set up a building and not have to worry about watching any more than one flank (something I disliked about cp_snowplow at first but that seemed to sort itself out). When it was only 1 engineer, after only a few kills the sentries were destroyed. Also, I think the class balance is nice in that area, as the building across from the 'sentry ledge' is far enough away that soldiers and snipers can take them out, and the windows overlooking the main well-styled-door can easily be spammed up into by a demoman using grenades or stickies.
So basically what I'm saying is that although a lot of people were complaining about it, I don't think it should be changed. This is what TF2 is all about, the fact that certain classes overpower others and yet there are still some who can counter said classes easily. Removing this would only unbalance the map and probably lead to a steamroll through the second point area (which is bad since 3rd point is right around the corner and there is usually still about 6 minutes on the clock).
So yeah, keep the engy spots. If there is a problem with it and more people complain, I suggest moving ammo around so that engineers need to move out into the open and are vulnerable several times.