The Oscorp tower missing in The Avengers and the Stark tower missing in TASM are not that big of a deal. Those are all really really really minor things. Heck, the Oscorp tower not always appearing in TASM's skyline is not that big of a deal either.
Even in real life, you will sometimes not see certain buildings in a major city's skyline depending on the angle from where you look at the skyline. Sure that there are a few exceptions like the Empire State Building and the WTC that can be seen from anywhere but that is because they're taller than most buildings in the city. The Baxter Building and Avengers Tower are not always present in NYC's skyline in all comics either. There are Spider-Man stories where you see Spidey on top of the Empire State observing the whole cities are the buildings aren't there.
Here's the thing, Stark Tower and Oscorp Tower both have in-universe fixed locations to real life ones.
In real life, Stark Tower would be on Park Avenue, above Grand Central Terminal.
Oscorp Tower is somewhere bordering east of 6th Avenue.
In The Avengers, they did a great job keeping Stark Tower in it's fixed location. In TASM, they did a piss poor job with Oscorp Tower for the most part. It isn't really a matter of angles obscuring, since I can point out to you the places where Oscorp Tower would be placed if you gave me some shots from The Avengers and same for Stark Tower in TASM.
Then again, I don't expect anyone who doesn't come from New York or studies the skyline to understand this lol.
So I dont think this would ruined anything for most people.
Don't get me started about the George Washington Bridge during the final swing.
I guess these can be more considered Productions errors rather than in-universe ones.
If Spidey being on the MetLife building is such a problem, you can always argue that the building isn't really gone but that the Stark Tower is just covering it in Avengers and the reason why you see it in TASM is because you see the city from a different angle. Same thing can be said about the lack of the Oscorp tower in Avengers.
On top of all that, you can also always say that TASM takes place before Avengers thus before the Stark tower was made. Sure that there are stuff like the date on the Bugle newspaper but does all that really matter in the long run? Marvel has already said they want to have the MCU keep going James Bond style just like the comics. The dates canon now will not be the dates canon in 10 years from now.
The thing is, the MetLife Building was carved into the Stark Tower, like carving a piece of wood into a sculpture.
Stark Tower IS the MetLife building. Apparently, that's the reason why it only took Stark 3-4 months to get Stark Tower built into the way it looked in The Avengers.
If the NYC skyline thing really is such a big continuity error, then I don't see why things like Howard Stark in CA:TFA is not. That would make Tony be in his 50's or older despite him looking younger and despite Marvel confirming that he was born in the very early 1970's. And if Tony is in his late 30's/early 40's at the moment, then that would put his dad in his early 20's in Captain America despite him not looking that young and despite not being treated as a guy that young. Howard Stark's presence in Captain America never made much sense. I know it was like that in the comics but it is one of those things that should be retconned or altered slightly by now (i.e. make Howard be Tony's grandfather instead). Yet for some reason, the GA didn't have a problem with it at all so I don't see why the small differences in the NYC skyline will have them up in arms.
There's still a huge chunk there contradicted and plus, X-Men Origins: Wolverine and X-Men: The Last Stand are still in canon for now. At least they're still considered in canon by Fox.
I think he looked in his 20s in CATFA....maybe even younger.