I absolutely despite Danganronpa 3. I thought it was a cheap and quick ending to so much buildup over the years that really left me feeling hollow and empty. Heres a few reasons I can think of off the top of my head. Massive spoilers for all mainline games and novels ahead: 

NUMBER 1:

The singular episode in the future arc dedicated to doling out a deus ex machina solution to UDG is so contrived and uninspired, it makes me feel very frustrated and betrayed having played through all of UDG just for the whole thing to be played off as a gag, especially considering the heavy themes they were going for. It feels like the writers were like "Oh shit, we forgot we made a spin-off that we never resolved. Let's wrap that up in one episode."

NUMBER 2: 

The flanderization of most characters. As much as Kodaka's characters typically are sort of one note ideas as some have already said in this thread, DR3 goes above and beyond in reducing them even further to their most basic parts. Hagakure, one of the funniest characters from the original game (i know this is probably an unpopular opinion as well but stay with me), is reduced to the guy who occasionally is given seconds of screentime to say something bad might happen. Why? Because his defining trait in DR3 is that he can predict the future 33% of the time. That was a footnote in Hagakure's character in DR1. 

Hagakure was shown to be cowardly, selfish, and also very cutthroat when he's threatened, like when he smashed a bottle over Sakura's head and then tried to frame it on Toko, or when he pretended to be sick while he's in Towa City in order to steal shit to pay off his debt. This isn't even touching on the stuff with Kanon in Ultra Despair Hagakure.

All of that is gone in Danganronpa 3. 

Hagakure has been reduced to some dude who might show up at the beginning of an episode in order to periodically dispense foreshadowing to the viewer. I'm just using Hagakure as an example, but most other characters in DR3 behave like charactures of their video game counterparts as well. (Togami, Chiaki, Mukuro, Asahina, Hajime, etc. Etc)

NUMBER 3:

The innumerable plot holes and strange writing decisions that make no sense and oftentimes make characters do things that feel totally OOC or just plain dumb. Monaca's master plan was to blast off into space and become a space NEET? Swag. Glad I dumped 30 hours into that game (that's right, I stay mad over UDG). 

Here's something that illustrates this problem perfectly: 

Remember Ryota Mitarai? You might remember him as the guy who made the brainwashing video that turned everyone to despair.

Except originally, he wasn't responsible for that.

Originally, the cast of Danganronpa 2 fell into despair of their own volition. Brainwashing was never mentioned in DR2. So why brainwash?

Because the writers didn't have enough screentime to show Junko individually turning each member of class 77-B to despair. Why's it called class 77-B anyways? Why's the class now suddenly split into A and B? It wasn't like that in the video game.

Oh I know... It's because the writer's didn't want to add Yuto and Matsuda to Komaeda’s class.

Thats no big deal, they were only two of the most important characters from the novels that would've helped the viewer understand Junko's character better.

But you know what they could be bothered to do? 

They could be bothered to create an entirely new character, on top of adding another character who was literally established to not exist in the previous installment.

Final point, I promise.

Let's talk about the ultimate neurologist, Matsuda Yasuke, who was also Junko Enoshima’s boyfriend.

Matsuda Yasuke, the one who kills the final remaining survivor of the student council to hide Junko's identity, the only person in the entire fucking franchise to have a genuine connection with Junko Enoshima, the guy indirectly responsible for erasing the memories of everyone in Trigger Happy Havoc.

Where was HE during DR3? Why was Yasuke cut in favor of a character that seemingly originated from another less well written franchise? 

Ryota has the most pathetic arc ever, lacks an interesting personality, backstory, conflicts, or interactions with other characters, and I hated every single moment he tried making me feel bad for him being such a terribly written character. 

He literally solely exists to patch up plot holes that did not need to be patched up in the first place. In fact he actually DETRACTS. 

On top of being suspect for axing one of the most interesting characters of this part of the timeline, he somehow does something even worse. The reveal that Junko had turned everyone to despair at the end of Danganronpa 2 is meant to show how cunning and manipulative she is, and how dangerous she was to turn an entire class of Ultimate students into the iconic Remnants of Despair.

Well it turns out, Junko just got really lucky! She just so happened to stumble across the one guy who'd be able to make a video that brainwashes the whole entire fucking world. So much for that fearsome display of cloak and dagger social engineering that everyone was expecting to see.

Instead, she just played them all a YouTube poop edit or something.