I loved the ending, actually, especially the after credits thing. That environment was freaking BEAUTIFUL Frictional. A++++!
The rest of what I have to say is spoiler worthy, lol so... spoilers I guess.
Spoiler below!
The only thing that made me angry was Simon's reaction. He knew that after the first time he transferred his mind that there would be another copy of him laying around. There was no taking his entire mind and putting it on the ARK so that the body he was in would just turn into an empty shell. Like Catherine said, it was a coin toss. One Simon went to the ARK, the other stayed behind, just like how the Original Simon ran off after his brain scan, eventually dying when his supposed cure didn't work, and the scanned Simon picked up his life after the WAU (I'm assuming the WAU brought Simon back to life) brought him back.
I hated how Simon just couldn't comprehend that he technically was on the ARK, but only the newest version of him. He could have been a little more understanding about it. I mean, yeah, he's stranded at the bottom of the ocean, but showing at least a LITTLE bit of competency in the regard that technically, he WAS on the ARK, would have been in my best interest.
Also, in that last cutscene, when the ARK is floating away from Earth, is the Earth on perpetual fire? Because honestly, at first glance it looks like the comet didn't hit at all, since there are only flare ups in certain areas on the planet, similar to how area's with higher population on Earth right now have clusters of light, whereas some places are dark since they have less population...
Anyway, I loved the ending, it was bittersweet and despite my qualms with how Simon reacted, it shows just how desperate his situation was, and reminds you about all the other people you might have left alive on the station to potentially live horribly for the rest of their lives, like Amy, who was just barely surviving off of the WAU's life support, and Lindwell, who was also barely surviving off of life support. If you left them alive, like I did, it makes you think about the Simon you had leave behind after the first scan, and how they may literally be suffering alone for the rest of their lives, however long that may be. How it was probably in your best interest to put them out of their misery, since they aren't living, they're merely existing and suffering.