I admit the execution was poorly done kinda, creating contradiction between the dictionary entries, some npcs and the story cutscenes, but the whole thing worked from a science fiction standpoint. Creating an universe within another and controlling it through super computer is 'doable'. Having people inside that manmade universe escape is also possible from a physical standpoint...hell, it's not different than lightspeed travel and wormhole.
Of course, if you see the Eternal Sphere as a huge binary computer, it's going to be lame, but that's not the case. It's no different than creating a blackhole and building an universe within that closed space. There is still a few problems with the "game" aspect of Eternal Sphere, but they play no importance in the story. You could literally omit it and story would still works.