You won't be downvoted, this sub is completely split 50/50 at the moment,
But seriously every single complaint you have for this game can be applied (or can't be applied in the case of stat/skill choices) to D3, so it's really tiresome to claim "Nostalgia! Nostalgia!" Rose tinted glasses only applies if people aren't remembering the game as it was, and since I still actively play D2, I assure you that I'm not wearing rose tinted glasses. I'm just simply having more fun with the game than I did Diablo 3. What the fuck is wrong with that? Why do I automatically have to be wearing some sweet shades for that to be true?
Stat allocation - Whether 99% of the builds were the same or not, doesn't matter. I had a choice and I made a choice actively upon each level up. Sometimes I'd fuck up, sometimes I'd go for a wonky build, but you're right - about 75% of my characters were "cookie cutter", as one would put them. Just like in Diablo 3.
Items - Diablo 2 had endgame items in the form of runewords as you said. What if you were too poor or too unlucky to obtain them? You had items usable at level 42 like The Oculus, Titan's Revenge, Homonuculus, Herald of Zakarum, etc.. that would fill that void effectively. Even if Diablo 3 had items like that, it's not much of a challenge to get - complete 6 missions and you're given an entire set of items that makes you OP.
Endgame - Every complaint about endgame from Diablo 2 seems to exclude the fact that there was PVP in the game. Sure, it wasn't much more than brawling, but it sure as hell wasn't a case of "ok you kill me in one hit, now I'll kill you in one hit". I had so many damn duels that lasted way too long because I'd run into builds that weren't gasp conventional or cookie cutter and would have no fucking idea how to deal with it. You didn't get hit once and die unless you were insanely undergeared for PVP.
Inventory - it's the exact same shit as Diablo 3 minus charms. If your complaint is that charms cluttered inventory, then you obviously prefer not having as many choices to customize your character - fair enough. I like choices. The more choices, the better. And it's not even an illusion of choice - I could stack FRW, or I could stack FHR, or I could stack all res, or I could stack life or MF or poison damage. The system could totally be done better today, of course, but Diablo 3 did zilch to improve on it, and at the end of the day it was another item drop that could potentially matter, and that's something that's very important in a loot driven ARPG.
Skills - I agree 100% that some sort of hotbar would make the game that much more enjoyable, but given when the game was released, it definitely wasn't a concern of mine.
Calling it a flawed game by today's standards is literally calling every smart phone that existed before Android or Iphone flawed. You can't make progress without having a baseline, and Diablo 1 and Diablo 2 were absolutely outstanding baselines.
All in all, I completely agree with you in that the game really shouldn't be remade or anything like that - Blizzard should keep moving forward with the series, even if I didn't like D3 and likely won't like D4 as a result, but some of your flaws are completely and utterly subjective and really perpetuate the "rose tinted glasses" argument that simply has no place against a game that still has an impressive player base for being 16 years old.