I can tell you why I have always loved MJ, and, therefore, MJ and Peter together.
MJ is a very well-rounded and realistic character. She's very pretty, yet not egotistical about it...she is, in fact, perhaps, even a bit insecure. She knows she's pretty, but her beauty is not her reason for being. Perhaps she's wise enough to know that outside beauty fades with time, but inside beauty remains. MJ is ambitious, and brave (how many times has she come to Pete's rescue?). As brave and independent as she is, however, she doesn't mind "her man" rescuing her from time to time! Her ego doesn't get in the way there, either. And she doesn't mind showing her own vulnerabilities (i.e., her tendency to run from a problem instead of staying to confront it). As a single woman, she hid pain behind an exhuberant personality, which was really just a facade for someone who needed someone to love, and who needed someone to love her in return. This makes her endearing. As a married woman, she was a devoted friend, partner, and companion. Most importantly, she loved Peter the science nerd more than Peter the Spider-man. One gets the impression that she couldn't care less that Peter is Spider-man, and that if he lost his powers tomorrow, she'd love him no less.
A well-rounded, well-thought out character. That she appeared as a constant in a comic book and still came across so real is amazing.
I'm not really the biggest comics fan (though I will admit to a sneaky love of the FF, from all the way back at the dawn of time, and I love Spidey and Torch together!)...but the draw for me in the Spider-Man comics through the years has been MJ first...and then MJ and Spidey together. A class act.
She's a great character...a rare character, and they are wonderful together. And doing what they have done is a very big and sad mistake.
Until she's back as his wife...I'm finished with the books and with Marvel.
Just a little P.S.: I love her friendship with Aunt May, too. How many mothers and daughters in law can communicate like these two do?