1. Is there any cloud solution you could use? Do you need THAT much media on your phone on it at the same time? Could you live with swapping it out (ie seasons of a tv show) daily? Base 32gb is nice, but given Samsung's history, anything else coming to the US is a big question mark. MicroSD cards aren't used by the vast majority given a good-sized internal storage solution, and they're slower and less reliable to boot - that's some solid reasoning for axing it when it didn't gel with the much, much improved design/build.
2. My bro's M7 is going on two years and hasn't shown much appreciable battery degradation. Keeping it topped off as much as possible will greatly lessen the amount it degrades over time. That said, I doubt it's gonna be too big a deal to get it replaced once every two years. This really shouldn't top your list of concerns, and I think you're placing too much emphasis on it tbh.
3. Nearly all phones are actually waterproof rated to a certain extent; enough to withstand brief rain or even light spills. It just isn't advertised to a ridiculous degree like Samsung did. What situations will you be using your phone beyond what I described in which it'll get drenched? Being careful eliminates most spills/toilet drops (hasn't happened to me in 4+ years). Waterproofing it likely would have had a noticeable downgrade on form factor/build materials/design. Definitely not worth keeping this from their standpoint.