Entirely different lenses for entirely different uses. Typically if you're using a tilt-shift for macro work it's something like product photography where you may need to get something like an entire plate in focus front-to-back, and you can take as much time as you need to get it exactly right. A faster, IS-equipped lens is more along the lines of things you have more limited & unpredictable time and conditions for, such as insects, or grabbing a quick close-up of rings at a wedding, stitched detail at a fashion show, etc. Of course reinforcing that is the fact the 100mm is full 1:1 while the new TS-Es are only 'half-macro', which further suggests the TS-Es being more intended for something like standard product (where you might be working in a smaller studio space so need close-focusing, but not true macro) and the 100mm is more for what we more typically think of 'macro' as being.
So as far as the different functionalities go, I think it should be a pretty easy decision to make. Shooting weddings, events, insects, flowers, or looking for something which can double as a general-purpose telephoto? Get the 100mm. Do you specifically need a tilt-shift? Then the 90mm or 135mm are your only options, and of the two the 90mm should have the most technical-neutral perspective and distortion (or lack of).
It is a little bizarre that one of the new TS-Es is 135mm, which is a focal length more commonly used for portraits and not often used in product photography due to the slight distortion and perspective compression, while 100mm (or equivalent, for larger format systems) is a more typical choice for such things. I can understand why the focal lengths would cause confusion. If I were to snap my fingers and magic up two lenses, I'd be giving the 135mm the IS and faster aperture and the 100mm would be sitting on a tilt-shift mount. But the TS-E 90mm to 100mm should be near-enough to not be noticeably different, and the 100mm for sure works well as a portrait/wedding/event/etc lens, so overall I'd just say hell, forget the TS-E 135mm exists. There are a few very niche uses for a tilt-shift lens longer than 100mm but they're so specialised (other than plain old 'because I can') that if you need it you'd already know it and not be questioning it. (And most of those uses usually rely on larger formats; it could be that Canon didn't bother introducing a longer TS-E until now because the 5DS R is their first camera which can realistically compete with larger formats.)
edit: disclaimer: I'm buying 'em all (the 90mm as a replacement for my well-worn existing TS-E 90mm; I already own the 100mm; the 135mm just because I dunno, it might prove fun to mess around with here and there) so I don't really have a horse in this race, so to speak.
