We'll probably never know for certain, but I think at least some of your complaints would have been addressed by the hour and ten minutes of material left in the editing room. Joss Whedon is a great story teller, but he also has a tendency to be very verbose, and I think in this case, that tendency came back and bit him in the ass when everyone around him (rightly) told him that people didn't want to sit through a three and a half hour movie in theaters.
Ultron was decidedly not nearly as charismatic as Loki or psychotic as Ronin or wacky as Justin Hammer, but I wouldn't dismiss him out of hand. I can follow the logic that he was built to protect the earth, and with his super-human intellect came to the conclusion that humans are a menace to themselves first and formost. It went off the rails for me when it stopped being that and turned into daddy issues.
As to Cap and Supes... it's not that we as fans don't want them any more... far from it in fact, if you listen to the myriad of arguments and complaints people still have about "Man of Steel" two years later. The problem is that the suits at Marvel and at DC are hyper-focused on a very small portion of the fan base; the fans of the 90's anti-heroes. To those folks, no one can simply be a hero to be a hero (see allstar superman) but must instead have some twisted psychological reason for doing what they do. And they crow and cry loudly that "Superman is Boring!"
For whatever reason knownst only to the suits, they chose to listen to this sector of the fanbase above all others, which is why we got the "now everyone is a grim and gritty batman" nu52, and a superman who is an emo whiney wrist cutter with daddy issues, and a captain america who is at odds not just with his timeline, but with pretty much everyone else in his universe. the new younger less grim and gritty batgirl and last year's big hero six seem to finally be signally a change in this idea, but progress is glacially slow in moving away from the pouches-and-steroids era thought process.
