I have mixed feelings about him, honestly. I think they did a lot of things right and a lot of things wrong. My biggest gripe is that it's too "anti-silver age". I think they took too many of the toys out of the sandbox to play with. I don't like the fact that he didn't grow up with powers as a kid. This bothers me a lot more than it should, honestly. Maybe it's because I grew up with the Ruby Spears Superman and that directly contradicts it, I don't know. It made it even harder to ignore because they went out of their way in the late nineties to remind you that he didn't develop powers until puberty every other issue. This was clearly done to remind you it's not the SA version. Almost out of spite. Especially when most of the time it didn't contribute anything of value to the plot. The one exception being Return of Superman where Lois used it to figure out that the cyborg was a fake. And that's not even canon anymore!
I like the "alien" nature of Krypton but it's story potential was clearly very limited. Byrne's Krypton was not a place anyone would want to remember, which was kind of the point but it also takes away from the mythos somewhat not having that well to tap into. I don't like the fact that he was on the football team. It just felt like cheating. Especially by then it was obvious he had powers. I don't like the fact that he was "born" on Earth. It was clearly another overreaction to the SA. We get it, you don't want him pining for Krypton. His antagonistic relationship with Batman got old quickly. Especially after it was obvious they knew each other for years. I didn't like the way they handled Supergirl. If you think Superman's history was a trainwreck, just take a look at hers. How hard would it be to do like the cartoon and just have her be from another planet with a red son passing herself off as his "cousin"? I also have issues with what removing the pre-Crisis version did to continuity. Everyone from Nightwing to the Legion was affected. Although I'm not a huge fan of the Legion, they still deserved to keep their history intact.
I like the fact that his parents were still alive. I like their Lex. I like the fact that he stayed on the farm instead of moving into town. Makes more sense for a kid growing up with powers to practice them in private. I like the fact that Clark was a more well-rounded person than before (although, to be fair, most of the cowardly nerd persona had mostly been dropped by the time COIE rolled around). I don't buy the "Clark is who I am, Superman is what I do" argument. I see them both as equals with different roles. Think George Reeves. I like the larger cast and story narratives. The original Cat Grant as someone who was in love with Clark Kent instead of Superman was a nice twist. Ron Troupe, Alice the office girl, Bibbo, etc. I also think their attempts to make him more "realistic" were somewhat selective. When half his rogues gallery is still aliens and magical beings, how "realistic" can he really be?
It was obvious by as early as the mid-nineties these limitations were putting a strain on story ideas. They were already trying to find ways to bring back some SA elements with Kandor and Krypto and the stuff they did for the sixtieth anniversary. I've said before you don't give him electrical powers and turn Metropolis into a futuristic wonderland because you have a ton of other ideas lined up. I think by about 1999 they started being a little more flexible about that sort of thing with stuff like Generations and Hypertime and Return to Krypton. But it's obvious that by 2000 they were looking for a way out and I think a lot of that had to do with the limitations that COIE put on him. This was also around the time Grant Morrison's Earth 2 came out which reintroduced the idea of the Crime Syndicate and the multiverse. Probably the nail in the post-Crisis coffin was Peter David's Many Happy Returns story with the pre-Crisis Supergirl. By then they were openly acknowledging the pre-Crisis universe existed. It even featured the pre-Crisis Superman! I don't think it's a coincidence Birthright came out around that time. It's obvious they were looking for a way out.