Here's an idea:

Using the Forecast enhancements as the baseline, beef up MDL7 to the most modern state possible, polish it, and freeze the format. After this, Conitec recruits a small team of beta testers with the specific task of testing a series of official MDL5/MDL7 plugins created for each of the major 3D programs. Create a user poll to determine the applications to support.

Conitec would no longer have to be concerned with potential engine conflicts because of some miniscule change made to a 3rd party format like FBX. It should also be simpler given it's native and has no bloat. Simply figure out what needs to be eliminated per application and export the appropriate MDL file that will work flawlessly. This would give users the greatest freedom of choice and should eliminate most if not all exporting problems from 3rd party programs.

I'm sure this would involve a fair amount of work, upfront, but once the deed is done, it's finished and upkeep should be that much easier. It would also be an expensive undertaking given the financial investment, however, the end result is a fantastic marketing bullet point, and the potential return from future users and "on the fence" upgraders should outweigh this initial investment.