I'm sure I'm one of many that have had fanciful ideas over the years of what could be done with Marylebone, the problem is, as ever, that it's so poorly located - Paddington is bad enough, but Marylebone is even worse. If you were to ignore that issue though, and for some reason you also wanted to ignore the fact terminal capacity is a waste, hence through tunnels being so in-vogue) the best I could come up with was to do a redevelopment deal with BNP Paribas to re-acquire the land on which their HQ sits, expand the station over it, and pull down the existing train shed and have a massive joint oversite development replacing it to compensate them. You would need to also pull down several buildings blocking the former gaps between the second set of tunnels out to Finchley Road, and then finally figure out how to get more tracks between Finchley Road and Neasden Junction. Gawd knows if the Chiltern mainline beyond that would have capacity for more trains though.
No, I suspect the best options would be to serve the suburban Chiltern services as part of Crossrail 1 from OOC (to get them out of Marylebone completely), then to operate the short remaining suburban services (such as Aylesbury via Harrow) using the 3 short western platforms, and the longer mainline services using the 3 long ones. Even better would be to run all the mainline services into Paddington's freed-up surface platforms, but I suspect platform demand there would put the kibosh on anything like that.