Originally Posted by
Mister Mets
I think the perception that they've been out of character is the result of two things that led to a bit of a culture clash.
The sliding time scale meant that Peter and MJ weren't much older in comics published in 2008 than they were in comics published in 1987. In that time, there were changes in terms of what's acceptable to depict in Spider-Man comics, especially when it comes to consenting unmarried adults.
There's also the odd coincidence that between Stan Lee's run and Brand New Day, writers from a particular generation had an outsized influence on the 616 Spider-Man. So writers born between 1948 and 1960 dominated from 1972 to 2007: Gerry Conway, Len Wein, Marv Wolfman, Peter David, Howard Mackie, JMS, David Michelinie, JM Dematteis, Tom Defalco, etc. There was an inevitable stylistic shift when a younger generation took over most of the stories (even though Slott, Kelly, Wells, and Waid were industry veterans.)