Bioshock Infinite's ending is just "bad", as it is when the same cop out is used in most mediums that decide to pull a giant time twisting paradox out to try and end things on a profound note when they otherwise write/design themselves into a corner. That said it's NOT as bad as the "Mass Effect 3" ending, nor does it come with the level of baggage (promises from the developers, etc...) that spawned "Retake Mass Effect" which continues to an extent until this day. "Worst Ever" doesn't fit it, since there have been far worse, again "Mass Effect 3" exists and it's going to take a really special kind of suck to ever outdo that one.
As far as the rest goes, picking on the right wing in Bioshock Infinite was both expected, just from the previews, and the apparent leanings of those doing the game. Anyone who was shocked by this probably should have paid more attention to the game they were buying. That said, in a nation largely polarized 50-50 on an idealistic level and arguably already headed towards a civil war by all accounts due to the time that deadlock has lasted, this was not the time or the place. What's more if your going to bring up these kinds of issues it's generally important to look at both sides of the equasion to an extent I don't think Bioshock does.
To put things into perspective, if your going to do a game looking at racism and want to have an "other side" at least do it right. Actually look at real racists for your inspiration, as opposed to creating cartoon characters based on stereotypes. Come up with fairly legitimate arguements behind it.
I'm going to play Devil's Advocate for a second here, so don't jump on me and try and argue the points I'm about to make because I don't agree with what I'm about to say. Though truthfully I'd argue down my own case a bit differant from most other people that would address it here.
If your going to defend racism, you can start with things like sociological arguements, showing how "white" societies and civilizations rose to dominance despite having literally everything stacked against them, where non-white societies and civilizations collapsed or decayed. Human civilization arguably started in "The Fertile Crescent" with dark skinned people enslaving whites for thousand of years. However when whites decided to get a leg up it started a trend that lead to the dominace of western powers which remained strong until the current era. Arguements about the destruction wrecked by white powers to keep the opposition down kind of fall flat when you consider how white civilization crawled out from under the wreckage of Rome. Not to mention how nations like Germany who for a time had the entire world against them managed to go from an artificially seperated, relatively weak and destitute society, back to being a world power, in relatively record time. Examining things globally you'll notice that non-whites outnumber whites greatly, but most of them wallow in poverty, backwards theocratic cultures that are deadlocked into themselves, and recovery or remaining where they are generally comes down to the morality and intervention of white powers. China, India, etc... rose up because White people let it happen and in many cases helped, despite a history of previous wars. Some places like Africa, The Middle East, etc.. are simply so barbaric that no amount of intervention, military or humanitarian, have managed to prevent them from being wastelands.
Outside of a sociological level, in looking at those nations, there is a more directly scientific arguement. Today you'll hear about studies saying there is no genetic differance between people of differant race, and that any claims to the contrary were debunked. In reality where you hear this, it's never really spelled out nor is the work of those who established the scientific rationales for racism ever truely debunked and indeed society continues to use their achievements, yet argueing they happened to be wrong about that. Guys like Mengele were maniacs, but very much believed in racism and inherant white superiority and was apparently able to prove it scientifically, engaging in things like Eugenic experimentation. Today we like to go off about how he chopped up thousands of still living people for his research and did all kinds of insane experiments, but we also save lives with information gained from the kind of research he did. The guys who pretty much discovered DNA, and whose work acts as the basis for all the DNA testing and such that we do now (proving crimes, etc...) were both also racists, I believe Watson (of Watson and Crick) was paticularly vocal about it and people try and gloss over that because it raises some uncomfortable questions while the guy is still alive and your using his work.
All of this can be counter-argued, but it can be more difficult than most people want to give it credit for. Instead liberals tends to like to simply leave it as "someone debunked it" or maintain a specific philsophy as an answer. In showing things that debunk a lot of this, it usually winds up avoiding direct confrontation because to say argue against Watson and Crick means you also have to argue against DNA and claim every criminal conviction obtained using it should be overturned, likewise you have to start saying guys like Mengele were wrong on a scientific level, which can be difficult because while the guy was a monster, we use information gathered by him (and other scientists of his ilk) to save lives every day.
If your going to build a hypothetical society based on a principle like racism, at least learn the dogma properly and look at what people are more likely to use. I suppose Bioshock gets a "pass" of sorts by being earlier down the time line than the examples I'm giving... but the point is that being cartoonish doesn't a point make. In general no matter how wrong someone or something might be, you have to understand that any major movement is going to have a lot behind it, and when the opposition simply dismisses that I think it leads to bigger problems down the road.
As I said, Devil's Advocate, I'm not going to argue any of this because I disagree with it myself so really couldn't push myself to "win" the arguement in any absolute sense and if I did it on an academic level I'd feel dirty afterwards. I'm just giving some examples.
Though to give a bit of "Nightmare Fuel" if your ever interested, take the points where "Infinite" touches on these issues (which it does, though it doesn't really follow through) but then extend it in the direction that Columbia actually works, as do the Vigors. It's far more advanced than anything else in that world except maybe Rapture, and apparently Comstock's guys know their genetics better than Ryan's guys did because as Yahtzee points out the "Vigors" seem to have dealt with most of the issues inherant in Ryan's technology. In the scope of the game I suppose it could be argued that your assumpsions are wrong and these "cartoonish" villains are right about a lot of things because they supposedly know DNA well enough where they are more qualified than anyone to make an uncontestable statement about racial inferiority/superiority going beyond anyone that really exists. On some levels there could arguably be seen as some validity to their arguements simply by the existance OF Columbia and it's attached technologies which they apparently understand as opposed to have just dimensionally scavenged. Definatly not intended, but on some odd levels it does present a slight example of bad writing/concept. Sort of like some science fiction where say the Nazis actually start eugentically producing supermen who have psionics and such due to their Aryan heritage as Hitler believed. The allies might fight them and win in the end but whe whole problem with "wierd world war II" and the Nazi stuff working is that it also implicitly involves an offhanded acknowlegement that Hitler was right... the writers don't even seem to realize that or follow through on it, but... well, that can get uncomfortable fast when you really think about it.
