At this point there are more issues with Miles Morales in 616 than in Ultimate Universe. In 616, he's Spider-Man alongside Peter.
So as far as "Miles and Peter co-existing in the same universe", that ship has sailed in all practical senses.
That's in the eye of the beholder.On top of that, he's essentially the rookie hero that is trying to live up to a more established legend, so when you put the two of them next to each other, he automatically seems to be the lesser of the two heroes.
The way I see it Miles Morales lends honor to the legacy of Spider-Man and Peter Parker.
Miles' success and presence is more of a threat to Peter, or at least one version of Peter, than vice versa.
Editorially, it becomes hard to sell the idea of Spider-Man as being a loser if a bright young smart kid like Miles openly identifies with and takes up Spider-Man's legacy. You can't dismiss Miles as a fan or a naive kid without coming across as well...you know. So obviously that means that Spider-Man is having a positive impact in Marvel. Likewise, you can't sell the idea of Peter Parker being a young guy who hasn't found himself and "mentally 15" when you have someone even younger than him flourishing and embodying that idea far more than he himself ever did.
So to me, Miles' success and him having a Spider-Man name is not a problem for him as a character. It's a problem for Peter Parker, specificaly a Peter Parker fenced-in editorially, as he has been since OMD. That version of Peter Parker (which never existed historicaly since it was dreamed into being editorially in the 2000s) is the problem.
Those examples are different. Miles Morales in less than 10 years has had a level of success in media adaptations and merchandising far beyond Kyle Rayner or Thunderstrike ever did. That success means he's here-to-stay. John Stewart, Green Lantern, is closer to the mark since the most enduring and defining version of Green Lantern is the one in the JLU cartoons. But even then that's not really the same thing.It's kind of like how DC had no idea what to do with Kyle Rayner after Hal Jordan came back or the struggles U.S. Agent and Thunderstrike had after they stopped being Captain America and Thor.
Miles Morales' success as a legacy character is quite unique and unprecedented and there aren't really comparable situations. For instance, people talked about Grant Morrison's Dick Grayson Batman. And yeah that was great and interesting but there has never been a cartoon show or a movie or a game where you play as Dick Grayson being Batman for the default. The only successful Batman series without Bruce Wayne in the outfit is Batman Beyond which had an OC Terry McGinnis in the outfit.
So it's hard to really arrive at some definite pattern with him.