I think the main problem is not the humans' attitude. After all, we have a history full of haughty self-centered bullies. The main problem, from a writing perspective, is that the humans get away with it every single time because Bioware says so. We have to take the writers' word for it and we have to believe the reasons they give make sense. Once or twice can be, but it all becomes too much. The best equivalent would be CKII's Sunset Invasion happening in real life. Unbelievable, isn't it?
And not only that, it's also sold as a positive value. When a human complains about the limits imposed to them, we are always given the option to sympathize. When it's aliens complaining, they are either weak, bitter, obstructive, out-dated or outright terrorists. Ok, ME1 tended to be more nuanced in that regard, with more options for Shepard to express their views regarding the issue. After all, however, the story gets more and more human-centric.
I realized the extent of it when I played Thane's loyality mission for the first time. When you think that a corrupt crook like Joram Talid has a point (trope!), it means that the writing team may not be sending such a convincing message as they think.
I see your point, and I agree.
Just because you CAN shout from the rooftops and give someone "what for!" doesn't mean you SHOULD, or that it's the best course of action.
But in the context of Mass Effect, we do see the negative AND positive of such defiance.
Humanity is considered to be a bit of a bully, which is why many members of differing species view humans with disdain, distrust, or outright hostility.
Even if you play as the Paragonest of Paragons, there is still a bit of friction there (and if your the Renegadiest Renegade, then heaven help you there).
The Reapers whole game plan relied heavily on the "lesser races" developing along a predetermined path, and that's why the Protheans were so "easily" conquered.
The current cycle was/is different because the civilizations were NOT homogenized, and humanity was/is very much leading the charge in that regard.
There's a phrase: "Any virtue taken to an extreme is a vice."
Each race has their own "virtue", but we see how that can be a bad thing.
The Asari are very patient, but it's that lengthy response time that ends up with them losing Thessia.
The Salarians are very knowledgeable, but taken too far is what resulted in the genophage being an acceptable military option.
The Turians are very stalwart and honorable, but have difficulty accepting anything other than their own opinions.
Whereas the Humans "virtue" is that they refuse to adhere to any one specific idea by default, of course, CERBERUS takes that idea and runs with it, and we all know what happened to them.
The reason that defiance is portrayed as mostly positive is because that is precisely what was needed to give the galaxy a fighting chance against the Reapers.
As to the reason a story like this is human-centric, a big part of it is that the writers all human (unless I'm mistaken). Even the best truly-alien characters are at least part-human for precisely that reason, and it's an ingrained part of our psyche to want to be more, to BE SOMETHING GREATER, which is where and why these tropes manifest themselves.
I note my bias as a human character in games where there's multiple options, and I prefer playing the "Hero" over the "Anti-Hero", so I note that bias as well; which is probably why I don't have any issue with the "HUMANS ARE SPECIAL" tropes.
But there are many reasons why those tropes are in play so often, as mentioned above. It's unreasonable to expect them to NOT be in these games in any capacity, and there are plenty of other games out there where you can play as a human (or not) and play as a pathetic scum-bag (or a clever jerk, or whatever) if that's what you really want to do.
I like Mass Effect for (among many things) it's ability to portray the positives AND negatives, and how sometimes they may not be what you think.
I also imagine that there's another species (I'll call them Hajokians) out there with a game like this and their fans are talking about how they want a game that doesn't have a "Hajokians Are Special", and if we ever meet them, it will be equal parts "Hey Neighbor!" and "Do I really sound like that?"