You're probably right, but examples like these, of a small team of PC-centric developers almost single-handedly saving a game from mediocrity, are so rare.
Not even the huge-budgeted Skyrim team could do it, as you've so eloquently written about.
Talented or not, Nixxes have proven that they can get shit done, for an apparently unprohibitive cost.
Think about this.
Eidos Montreal are making a game from scratch. They are taking an old engine and massively upgrading it in order to a) make it compatible with their new style of gameplay b) improve the tools for content creation c) make it look pretty. This is not a small task. On top of that, they are also building a huge (by today's standards) and highly detailed game that emphasizes player choices, multiple routes, etc. This is a gigantic task that most developers would try to shortcut (license Unreal, reuse art assets, etc.). Even without working on the game engine, Deus Ex is a bigger game than almost any other save for MMOs and full-on RPGs, and it has higher production values and expectations for quality, variety, etc. to boot.
Nixxes, meanwhile, have the prestigious job of a) setting up the PC controls b) getting the game to run smoothly on PC c) adding in DirectX 11 support and effects d) adding a few extra features and tinkering with the UI to get the game feeling more like a native PC game. Now, I don't want to discredit their work, because as I said I think the PC version of Human Revolution was quite good, but the fact is that even if they are a much smaller team, they also have a far smaller job. I don't purport to know the details of what they did, but somehow I doubt their undertaking was remotely comparable to the creation of the base game itself.
If you had switched their roles, with Eidos Montreal handling the port and Nixxes handling the main game, and had team sizes and budgets to account for that, would the result be any different? I don't know, maybe... but does that mean Eidos wouldn't do their research, get the game running smoothly and stably, and add in those extra features that fans were begging for?
Creating games is a business. While personal talent and ability does come into the equation (developers are teams of individuals, after all), if you are given a job to do like Nixxes were, unless they were flat-out incompetent I doubt the results would have been all that different. It's just too hard to say whether or not Nixxes "saved" Human Revolution on PC, because we don't know the details or how much of a labour of love it really was for them. For all we know, adding in an FOV option and DirectX 11 support was a mandate from the publishers, who were eager to please fans and felt it would increase sales (which it probably did). Who are the heroes in this scenario?
Going back to X-COM, I have a lot of faith in Firaxis. Say what you will about Civ V (whose problems were mostly on the design side and not the technical side), they know how to make PC games at the very least. The problem is they aren't making a PC game, at least not one that's necessarily native to the platform. If it was in their contract to do so, then I'm sure they'd love to make a UI and add all sorts of PC exclusive features... but at this stage, we just don't know exactly how it will turn out. I'm willing to bet, however, that the answer is "no." Honestly, though, it may not matter. You might have fallen in love with the X-COM interface, but that doesn't make it the best ever simply because you're so used to it. I highly doubt Firaxis would keep things identical even if it were a native PC game, simply because the needs of their game are different and conventions (which can't really be measured objectively) have changed.