The only thing that Master Collection gave us that purchase all build targets didn't was assurance that any future paid features would be available to people who had shelled out for MC, without having to spend any additional $$$. For me, that was worth it, even though I never used Mac OS, iOS, Android, Tizen, etc.. I bought into MC when it was still only $599, and benefitted by being entitled to all the additional paid features YYG released over the next several years. When YYC came out, I didn't have to pay for it, and I would have been angry if I had to.
For GMS2, I'm only intending to purchase Desktop and HTML5, and am unlikely to ever buy Mobile, UWP, or Console build targets, unless I end up working on a commercial project that will pay for it. But if there was a Master Collection option that assured me that I could get everything else that YYG might release at a later date, and it was priced at a bundle discount relative to purchasing all modules individually, I'd likely buy it.
But I do like, under the current pricing model, being able to upgrade to GMS2 Desktop + HTML5 for only $125.
(Why you gotta charge so much for HTML5 tho?)