I think once the Thruway goes all electronic for its tolling, the notion of having separate exit numbers for I-90 and I-87 will be a lot easier.
Somewhat easier. You still have institutional inertia, which is a real thing in New York.
^ Some states up here have already asked FHWA for exemptions and waivers. I know Vermont did a few years ago. They were politely told "no".
Precisely. It's going to happen whether people like it or not. There is no reason to not change other than people being reluctant to change. If a slow change is what's necessary to make people warm up to it, so be it. Better than MA, which planned a change and then had to back down due to public outcry.
As for the Thruway...given the typical distance between exits, there is absolutely no reason why they couldn't make the Thruway exit numbers mileage-based.
The mainline has no exits closer than a mile north of Westchester County. Even then, you could fudge some numbers to make only a couple of A/B pairs necessary.