Box Office: The Avengers> Avengers 2 > Iron Man 3 > Captain America 3

Actually I don't think the numbers bear that out. Just because a sequel doesn't match its predecessor doesn't mean a genre is in "decline". For one there are more superhero films around these days meaning that competition drives individual grosses down, but that is not necessarily an indicator for the health of the genre. There are five superhero films currently in the top 11, which doesn't look like a waning genre to me.

Because Iron Man 3 was released before Avengers 2,I'm not 100% sure to understand the logic.

Are you saying:

The Avengers> Avengers 2, Iron Man 3 > Captain America 3 ?

That could be a sign yes, that for at least those iteration a mix of fatigue, but also a big resistance (some audience will think, hey I didn't saw the last one or the last 2 or the last 7, can I see this and follow this one ?) Isolated title are probably a better canary for the genre and both Dr. Strange/Suicide Squad did really well this year.

And the opening of those that arguably underperformed like BvS show a demand, Suicide Squad first friday was a crazy one too.

2008:
Dark Knight 1003, Hancock: 624.4, Iron Man: 585.2, Hulk: 263.4,
Total: 2.47 billion, Average 619 million by movie.

2009:
X-men: 373.1,
Total: 373

2010:
Iron man 2: 623.9
Total: 624

2011:
Thor: 449.3, Cap America: 370.6, X-Men: 353.6 Green lantern
Total: 1.17 billion

2012:
Avenger: 1,518.8, Batman: $1,084.9, Spider Man: 757.9
Total: 3.361 billion

2013:
Iron Man: 1,276.5, Superman: 668.0, Thor: 644.6, X-Men: 414.8,
Total: 3.004 billion

2014:
Guardian: 773.3, X-Men: 747.9, Spider-Man: 709, Captain American: 714
Total: 2.94 billion

2015:
Ultron: 1,405 Ant-Man: 519.3 Fantastic 4: 167
Total: 2.087 billion

2016:
Civil war: 1.153 BvS: 873.3 Deadpool: 782.6 Suicide Squad 745.6 DcStrange: 619.4 X-Men 543.9

Total: 4.718 billion with some DrStrange still to go.

An argument could be made that it was the best year for superheroes movie at the box office, with the 2013/early 2014 exchange rate, Civil war would probably be above iron man 3, BvS around 1 billion, Suicide Squad above 800, DrStrange would finish over there and X-Men not as far of the previous entry at over 625.

And the other year's tend to have some flop in there, none in 2016 except if we count ninja turtle as superheroes.

No genre/franchise lasts forever.

All of the great properties, franchises, and genres have gone on hiatus at one point or another, fallen out of popularity in a big or small way, undergone some kind of reboot, etc etc.

The superhero genre will not remain 'on top' forever. Heck, once could argue that it being the 'top dog' at the box office is already a thing that came and went.

2008 saw The Dark Knight become #3 domestic and what, #4 worldwide?

2012 saw The Avengers lock in #3 domestic and #3 worldwide. No superhero film has reached those heights, or gone higher, since.

2015 - Jurassic World hit #3 domestic and #3 worldwide....and then Star Wars reached #1 domestic and #3 worldwide.

So The Avengers continues to be pushed down the ranks, and while Infinity War and Avengers 4 will be huge, I don't see them being as huge as Star Wars: The Force Awakens globally, or reaching Avatar numbers in North America.