We\'ve decided to create a custom bootstrapper for our deployment solution. We are currently re-writing and re-designing our deployment strategy for all of our products. Sad
Frankly, Burn isn't going to be done for at least a year. You already have InstallShield and IMO it has the best off the shelf bootstrapper currently available. I'd scope your requirements back and make it fit the box. Pretty much everything I read from you can be done using InstallShield if you learn to push it to it's limits.
I would go for Burn anyway or some already existing solution.
I'm sure that after some time you'll face new problems that you can't now really imagine. If you face them, that means that Burn's developers have already faced them and probably got them solved. If not, Burn has a large community that will fix the potential bug faster than you.
Focus on the software you're developing, not on writing installer/bootstrapper.
If I were in your shoes, I would give a burn a try. I'd get me a couple of days and see if it meets my requirements.