Danganronpa for me and it's not even close. Fast-paced, trope subversions, style; pretty much everything about it was made for me. And on top of all that, V3 did something that I've never seen before in any work of fiction regardless of medium and I'm still thinking about it weeks later. I'm probably going to make a thread about it when more people have completed the game.
Zero Escape is good, but it (and Uchikoshi games in general) are VERY end-heavy. I was bored of 999 until around the end of the safe route, and I got all the other endings before that after being recommended to do so. VLR and ZTD are a bit better in terms of the mystery being sprinkled throughout the game instead of just the ending, but even they have long patches of boring.
Ace Attorney is good, but kind of redundant in a lot of ways and many cases are completely hit or miss. And as far as overarching plots go, they're honestly just not that interesting.
Steins;Gate has a great second half, but it shouldn't take a boring nothing of a first half to get there. And on top of that, Steins;Gate Zero is super underwhelming in terms of overall mystery revelations.
So yeah, giving it to Danganronpa. 3 still sucks though.
Edit: If I HAD to assign a ranking, it would probably be DR>>>>>>>>>>>>>ZE>AA
I don't think putting Steins;Gate in the ranking is very fair since it's just 2 games while the others have 3+. I guess if we were going by individual game rankings, S;G would be somewhere in the middle after all the DRs, 999 and the first AA, but in front of everything else.