That always seems to have been a big problem for Marvel in the past (though it's also plagued DC as well). Continuity gets too big for its own britches combined with the fact that some writers on certain books throw out plot twists not to write a good story mind you, but more in the name of shock value as a way to thinly veil their poor writing chops.
Back in the 90's, 616 continuity had just that problem and then some with characters newer readers couldn't really relate to and the fact that while nerd-dom was flocking towards cool badass characters in leather outfits who looked like and spoke like real people, Marvel at the time was still publishing stories that read more like a kid's wild imagination with one dimensional goofy villains saying narmy things you would expect to see in a Saturday morning cartoon, not a comic book
i.e think about every time Mystery Inc. on Scooby Doo busts the bad guy of the week, he/she always cries that if it weren't for those meddling kids and their dog, he/she would've gotten way with their plan.
Hence the creation of Marvel's "Ultimate" Universe in 2000. An alternate universe where Spider-Man, X-Men, the Avengers, and the Fantastic Four went back to square one in their super hero careers, but in the then modern times of the Turn of the Millennium with simplified origin stories and more plausible explanations for most everything. No prior explanation as to why, no prior knowledge of the character needed. Nothing. Just a simple universe where you could easily get caught up on what was going on in a few days at most. Fans of the MCU owe it to the Ultimate Universe for why the MCU even began in the first place.
Much like the Ultimate Universe in its heyday, the MCU too is a place where you need to have no prior knowledge of who's who and can reasonably get caught up in about a week or two without having to worry about continuity all that much. That said, the MCU tends to draw more from the classic 616 verse than it does Ultimate although certain elements of Ultimate are used like Cap and Bucky being childhood friends, Tony Stark's MCU personality portrayal drawing more from Ultimate Tony Stark (him being an egotistical shameless drunken womanizer) as opposed to 616 Tony Stark though the 616 origin is used, and of course, Nick Fury and S.H.I.E.L.D being the reason for why the Avengers assembled (though even that uses Loki as part of the reason why much like 616)
However, all good things have to come to an end and by the mid 2000's the Ultimate Universe slowly began to lose its luster as elements that made it unique compared to 616 started being incorporated in 616 such as its distinct slower paced cinematic style of storytelling. Combined with terrible writers on certain books cough Ultimates 3, Ultimatum cough and the fact that after Ultimatum, it became a hassle to catch up on events to learn why Reed Richards turned evil or why there's a black Spider-Man swinging around town, its probably no wonder why Marvel chose to cancel it earlier this year during the 2015 Secret Wars company event. After all, 616 became far easier to follow once it took what made Ultimate so good early on and with the MCU combining the best of both 616 and Ultimate, Marvel's once critically acclaimed alternate universe outlived its purpose.
tl;dr 616 used to have the problem of being uber bloated and too complex to follow and ironically enough, Marvel's answer to that, the Ultimate Universe which was made with the intent of simplifying things that 616 made confusing started having that problem in its later years until it was canceled in 2015. MCU is doing fine so far with being easy enough to plausibly catch up on in a matter of days even if you've never read a comic book before in your life, though now that we are on Phase 3 of the MCU not to mention all those TV shows we've got like AoS, Daredevil, and now Jessica Jones (with more on the way), it shall be interesting to see if the MCU will suffer the same problem or not.
