The Leica M will probably have solutions to address some of those issues, like offset microlenses and thin IR filters and no OLP-filtering.
I presume that future M lenses are designed with digital sensors on mind.
You have quite rightly pointed out some hardware fixes to problems with some existing M-series lenses. My tests
indicate that some errors are somewhat correlated with ray angle. One way to make things better with new lens designs would be to go to a retrofocus layout to get the ray angle of incidence to the sensor closer to normal (in the geometric sense of the word). However, that would mean giving up the desirable compactness of the M-series lenses.
I'm sure there will be people who will cringe at the very suggestion, but I think a fruitful avenue for the Leica M camera designers will be firmware that's aware of the vicissitudes of each lens when coupled with the sensor of that model camera, and will make appropriate corrections. I think Leica does some of that already. I think it's working pretty well in the RX-1. I suspect from the relative lack of corner color, that Sony is doing some corrections for the 16mm lens in the NEX-7.
Some firmware corrections may cause a loss of resolution, but sensor resolution vs time is still on a pretty steep slope, and soon we'll have sensors that can out-resolve the lenses, at least in the corners, where there will be the greatest need for correction.
A drawback for Leica of putting most of their efforts behind a firmware-based approach might be that there would be little reason for its customers to go out and buy new glass. However, there's a base of customers who have large investments in Leica lenses, and the company would be well-advised to do what it can to keep those people in the fold. If the price of getting the best results is buying new lenses, many people might take the opportunity to jump ship to another vendor.
The issue of third-party glass is thorny. Leica won't want to do things to encourage its customers to buy Zeiss lenses. They could come up with a scheme that allowed customers to load plugins into the camera, but that doesn't sound like Leica. My guess is that the corrections for third-party lenses will be done in programs like Lightroom, and that Zeiss will make available Lightroom correction plugins for each body/lens combination that has a large enough customer footprint.
It's an exciting time to be a photographer.