I think... it seems like a lot of your frustrations stem from Multiplayer. I'll be honest, I only played Multiplayer a few times due to a lack of people with the game, so I didn't really run into those issues. Similarly, I didn't do Mission Mode until I was already done with the game, and was grinding levels to get Lv 99. So it wasn't a big deal that I was redoing challenges... cause I was already just grinding which I find boring as is. With all that said, I didn't really play as the other characters that often, so I didn't really run into the issues you mention about Lexaeus vs. Zexion or so forth. I have so little to offer on the multiplayer front that I find it hard to counter your arguments. It seem that your frustration with story mode stems from playing multiplayer and single player concurrently, whereas when I played the game I did SM on it's own. I liked the mission format, as it allowed for bite sized encounters across a variety of worlds. In the same way that Mario has short levels on handhelds, or that each Pokemon trainer is like it's own little encounter, Days allowed for short playtimes that complemented the DS' portability. The 10 minute drive to school could be a mission or two, the hour long trip to Grandma's could be a few days. Players could pick and choose how far along in the game they wanted to go, allowing for greater player freedom.
Speaking of player freedom, that's exactly what the Panel system is. Instead of giving you armor slots, or a command menu, or the same old leveling up and equipping system used in hundreds of other RPGs, Days brought something new to the table. It asked you to look at the mission you were about to take on, and plan your kit accordingly. It's like... if you play a game like Payday, you're not going to bring a flamethrower to a stealth mission. In Days, it's different from other KH games. It asks you to plan ahead. "Here's the Heartless, here's the location, prepare for Ice Cubes". Instead of just straight levelling up like in Kingdom Hearts 3, or just choosing the strongest keyblade like in BBS, Days gives you options. This Keyblade deals more crits, this one has high defense. While I can't deny that some enemies are frustrating to deal with, and a good portion are damage sponges, there is incentive to plan your kit around specific heartless and plan ahead of time. Not just that, but adding Level ups into the panel pool is really inspired. In nearly every other JRPG, when you level up, that's it; you level up. But in Days, when you level up it's simply an option. It kinda reminds me of TWEWY, where you can change your level for added challenge, or for better drops. In Days, if you want a challenge, you can always take out the level up panels. Sometimes you might be forced to choose between a level up or something vital, and I find that freedom of choice fascinating and fun. It's not going to be loved by everyone, but it's at the very least a well made and well balanced gameplay mechanic. With magic, that's harder to say. As I mentioned, I didn't really play as the other characters. I only really played as Roxas. And so... my perspective on magic is different. I found magic to be something I hardly ever used. I brought it if I needed it, or I just didn't. Sometimes, I would bring tons of magic to fight a specific enemy, other times I wouldn't. It's different than other KH games... which is why I think some people don't like it. It's like a proto-command system, except the magic doesn't just charge back up. I found that awesome, because it asks the player to think critically about their magic use, and be more careful when using it.
I can't refute anything you said about BBS multiplayer because... guess what! Never played it either. But... at least what I heard from my friends was that it kinda sucked. So heresay. Sorry.
The unbalanced characters in mission mode? I always thought they were just fun additions, and never really put how balanced each one was to my mind.
I think that Days actually has a surprising amount of variety in enemy types. There's 24 different heartless types (not including some of the later bosses, of which there are 10, not counting recolors) and that's a pretty good amount. But then there's "recolors" that add a lot to the game. When a heartless gets recolored in Days, it doesn't just look different, it plays different too. Compare Yellow Operas to Emerald Serenades, Hover Ghosts to Living Pods, and you'll see what I mean. They react differently, move differently, attack differently. And that actually adds a lot to combat! In comparison, BBS has 24 types of unversed... and that's it. No recolors with different elements, no interesting ways to take them down. Just 24 enemy types across 3 storylines. Plus, in Days, you can throw in two types of Nobodies for basic enemies and then you've got tons of great bosses. Everyone always remembers fights like the Leechgrave (who I agree is not fun to fight, even though I love the concept) and the dreadful Ruler of the Sky, but that's also amazing fights with Saix, Riku, Xigbar, the Xion battles, Pete, and a few fun heartless bosses for the cherry on top. Plus, early mission have tough fights that you can either do then, or come back to later.
I dunno if I agree with you on BBS though. While Days doesn't give us too much insight into the Organization's specific members, it gives us the best look at a single group of characters in franchise history. Axel, Roxas and Xion get an amazing amount of character depth, and Saix gets built as one of the best antagonists in the franchise through his constant douchiness. I understand where you're coming from a lot of your points, I just disagree that they are as clear cut and unarguable as you make them seem.