Cap is a very core part of the Marvel Universe though, less so than Cyclops, and the FF are contained in their own niche. Cap is also an early creation of Jack Kirby, and a Golden Age character who's survived the best through the years for Marvel's pantheon. He fully deserves his spot. I may not like him all the time, but I have to give him respect.
If I had to pick 12 characters to make up Marvel's JLA, I'd go with a mix of powers, position and popularity.
Human Torch I
Doc Strange/Captain Marvel--I get the feeling that Marvel very much wants Genis to succeed commercially, just they can't figure out how to properly market things.
Daredevil/Black Panther--BP for the same reason as Captain Marvel.
At first we have the Golden Age triumverate, then the founding members of the Avengers, who were all big sells back in the day, as was Doc Strange. Wolverine is arguably the most popular mutant, though I feel some of the originals should be on the list, but for so few numbers, they just don't cut the mustard. Spidey and DD have both held a steady monthy title, at least, throughout the years, and are staple Marvel characters, as I feel Marvel wants BP to be as well. Wish they had a few more well developed female characters though. I think She-Hulk's come into her own as a strong central character, but we need some more.
scarlet witch(house of M)
spider-woman 3(has all the powers of any previous spider woman and telepathy and clarvoyance, and pregognative abilities)
Well there are a myriad of ways to look at it. Many of DC's characters have Golden Age roots, a period of comics that has been much more streamlined into DC continuity. Batman, Superman, Wonder Woman and more were all around in the 40s. Most of Marvel's main heroes today weren't.
From a Golden Age standpoint:
Dynamic Man = Superman
Challenger = Batman
Miss America = Wonderwoman
The Vision I (Aarkus) = Martian Manhunter
Namor = Aquaman
Can't find anyone specific, though undoubtedly one of the many mystics could fill the role, or perhaps the Fiery Mask = Green Lantern
Makkari retroactively, Hurricane or Mercury in actuality = Flash
Hawkeye = Green Arrow
Black Fury/Miss Fury = Black Canary
Timely comics had more mystics than Sally Struthers has chins. = Zatanna
Red Raven = Hawkman
Thin Man = Plasticman
That's just for analagous powers. I could go more into popularity and cultural significance, but I won't.