Marvel Comics never had an explicit framework for how their timeline worked, instead just sort of choosing to ignore historical contradictions. It didn't matter that Mr. Fantastic once served in WWII. They just never mention it again and it sort of goes away. I'm afraid I'm a lot more anal than that, though, and just had to put some thought into how I would explain these contradictions in Make My Marvel.
I think I've hit on the idea, something I'm calling 'Compressed Time.'
The basic (and only) idea is that the only way to rationalize 50 years of monthly comics is to instead consider them 10 years of weekly comics. How's this work? Well, in very broad brush strokes, we'll assume that each successive issue of a comic takes place the week following the previous issue rather than the next month. For example, the Fantastic Four debuted November 1, 1961 facing off against the Mole Man in 'Fantastic Four #1.' Their first encounter with the Skrulls in 'Fantastic Four #2' would then occur about a week later, on or around November 8, 1961.
Sure many comics are continuations of the issue that came before, requiring only minutes or hours to have passed, but enough comics have vague spacings that I'm sure could even things out over time.
The big kicker of this whole concept is that, with Make My Marvel having a soft kick-off at roughly the end of Secret Invasion (January, 2009), that means only 567 weeks of Compressed Time have passed since the debut of the Fantastic Four. In other words, the adventures we're reading about now are actually taking place in September of 1972.
There are a few anachronisms that come with this concept, such as the number of presidents our heroes have encountered, or the tri-monthly Christmas adventure, but these are no less jarring than the actual number of presidents Captain America has met since thawing out (or the number of Christmases he's celebrated since appearing in the "modern day.") Technological advances, in comparison, are much easier to accept. With minds like Tony Stark and Reed Richards pushing the envelope, the development of the iPod in 1971 is pretty easy.
But once you accept the plausibility of Compressed Time, a few interesting alignments start to appear:
After their heroic debut in November of 1961, Reed Richards and Sue Storm would get married less than a year later in September 1962. Exactly nine months later, Franklin would be born (June 1963). Per this timeline, Franklin is only about 9 years old now, which seems in keeping with his apparent age in the comics.

An interesting Spider-extrapolation is to notice that, even if Pete and MJ had a baby tomorrow, the earliest they could have a 15-year-old daughter is 1987-ish, creating a soft start time for Spider-Girl and the MC2 universe.

There are probably a lot more fun timepoints to plant in Compressed Time, but those will do for now.
Admittedly, there are some current second gen characters which might cause some hiccups, though. Wiccan and Speed of the Young Avengers get a pass for the bizarre nature of their recreation. Fellow teammate Hulkling was supposedly conceived only 8 years ago, but we can call that an accelerated Skrull development. Likewise, Reed and Sue's second child, Valeria, was only born a year ago according to Compressed Time, and she's depicted as obviously older than that. I wasn't reading FF when she was written, but Wikipedia tells me there were some cosmic, Franklin-related shenanigans to her birth that might serve as an explanation to her advanced aging.