I agree on Clover, Alice, Kyle missing being dumb. They definitely didn't completely clean house with this game. I don't know if it's rushed or if he didn't actually have a plan for all those characters in a 3rd game.
The alien machine is dumb, but also, see above about the whole series having shit like that. Morphogenetic fields and shifting were just as tongue-in-cheek when I first heard about them. They just look less ridiculous now that ZTD utilizes them from the start. They needed a literal machine to wrap the story up, I've allowed so much ridiculousness to happen without putting the game/series down yet, so I just shrugged and went with it
Radical-6 is not a foregone conclusion in ZTD, they prevent it in the final ending. Now they have to go kill a terrorist or something....I really don't know if I want ZE4, but some kind of non-escape room psychic shifting terrorist hunt might be interesting.
Akane is not the same "EHH JUMPY KAWAII SEX JOKE" she was in 999 at all. Maybe not as on point as the older version in VLR, but by the end she takes control of pretty much everything up through the ending and becomes the defacto leader of the whole group. Not sure how anyone playing missed this. I think I did C team last so there was a pretty clear progression there to me.
I thought they pretty clearly explained why Junpei was the way he is and it's not much of a heel turn, he's just cynical after having to go through terrible shit to save a girl who disappears. Then he does classic risk-taking behavior with his detective job that makes him even more hardened. I can see it. Reality is that not everyone comes out of a traumatic event all positive and filled with anime determination. Sigma is a pretty melancholy guy in the same way.
Phi and Sigma knew what they were doing and were there to assist Diana and keep her from the one ending where she brings Phi to the top. Makes sense that the they show you the one that leads to VLR.
As for the villain, he's honestly no more stupid than Akane and Akane/Sigma from the previous games, who also devised ridiculously convoluted and extremely evil plans to accomplish some greater goal. I don't understand how one could hate him and not the others. He's right in line with Zero not actually being some ultimate evil, but actually a good guy in disguise. He's just more on the edge and not as motherly as Akane in explaining everything.
Mind hacking was definitely silly as fuck though. Delta is silly as fuck but kind of hilarious.
also I found Eric and Mira to be very memorable, but definitely pointless