I know exactly what you mean, Majin. It always seems to happen to my team on Dustbowl stage 1 CP2, assuming we don't cap it straight away. You'd think a good tactic would be to hole up in the tunnel on the left and charge a few ubers, but we always end up getting hit from behind by some random critikaze soldier.
However the answer IS always ubers (after organisation, of course). Ubers thick and fast. Make sure your team has 2-3 medics, and make sure above anything that they don't die until they pop their uber. Go for the double or triple uber if you can, but don't go too far out of your way for it. A single uber with backup is usually more than effective enough (if the uberee is any good).
It's all about the situation. If they've go a tonne of sentries, uber a demo and take them all out, then attack while they recover. If it's just a really defensible point like Dustbowl stage 1 CP2 (after they get defences up, anyway), uber a heavy or pyro, and concentrate on fending them away from the point and covering your teammates as they cap rather than rushing their spawn or whatever else you might want to do. And while you're at it, join in the discussion on the
uber guide - there's a lot of sense between Samadhir's ears (ololol).