I think I just "beat" the game this morning. I may have had a better experience with it than some though, since I was actually aware that mission 46 is technically the "last" mission as far as story goes. So knowing that, I may have just been able to appreciate it a little more.
I totally agree that the story as a whole was really weak. The stuff about the parasites was just... long in the tooth. So much prattling on about it, with almost nothing actually happening with it. And everything in the first chapter (the first twenty something missions) seems really loose and unfocused now that I'm looking back on it. It may have just been the fact that I stretched all of this out over 138 hours (holy shit, longest I've ever spent on any game in one playthrough), but judging by Riku's scant 50-hour time and his resulting thoughts, I'm thinking that's not really the case.
Anyway, whoever it was (too lazy to look right now) that said that it seemed like Kojima just had a bunch of ideas for scenes in his head with no plan on how to fit them together... that actually seems about right. There really are some excellent scenes here and there, definitely a number that will stay with me for a long time, just as the rest of the series has. But there just aren't enough of them, and they're all so far apart that you almost start to forget there even is a story.
Have to say I actually really loved the twist though. I was thinking for the whole game that it was going to be something else entirely, but then it kind of threw me for a loop. And as nutty as it is, the now-traditional timeline at the end actually shows that it totally fits within the series as a whole. The game does feel like it just kind of ends with no build-up or climax, but the timeline and the twist do manage to bring the series full-circle; there might be some gaps to fill in or whatever, but it's mostly stuff that only needs to be told and not shown. Surprisingly, MGSV really does bring the series to a sort of close, just as I was hoping Kojima would pull off. The story of the game itself is obviously "unfinished" to a degree, but when considering its place within the full series timeline, it actually segues right into the original Metal Gear.
I'm not going to comment on everything yet, because I still haven't seen some things (this "rain scene" with Quiet hasn't happened yet for me, and I haven't quite finished everything with the "secret" side-story on the medical platform), but I just thought I drop my basic thoughts post-credits. I think it'll actually be about a year or two before I can really place how I feel about the whole thing, but it's certainly got its ups and downs as it stands now.