Thoughts:
1) B-29 is going to be perked, and HEAVILY. I'm expecting to see it as at LEAST 200 perks, maybe as high as 500.
2) Just like any other 4-engine bomber, the B-29 is going to take time to get to altitude. Which means anyone rolling a B-29 from a forward base is going to be low and struggling to get air underneath them as they cross the front lines.
3) The B-29 is STILL a fast bird at all altitudes, so she doesn't necessarily have to climb to 30,000ft to make life difficult for defenders. Remember that the B-29 WAS used in the same sort of low-altitude, high-speed night raids the Mossie B carried out in Europe.
4) There's still question as to how HTC will model the gun controls.
5) In all likelihood, B-29 sorties will be launched from bases deeper behind the front lines, so it SHOULD be easy to spot a high-altitude B-29 raid forming. One can generally assume that the altitude of such raids will be "high" and can be planned upon accordingly.
6) While the B-29 IS going to be used to hit bases, it's almost guaranteed that she's primarily going to be used to bomb the cities and HQ, so it's not going to take a WHOLE lot of guesswork where those high-altitude B-29 raids are heading. This should actually PROMOTE combat, assuming people want to up to defend the city and HQ.
Remember, as long as you roll to oppose them, bombers will ALWAYS promote a fight.