Neither way is the right way to tell which is better. Games are art and art is subjective. However:
-Skyrim has far more Base Content than MW3, and has had a longer development cycle and more work put into it.
-Skyrim on the PC does not look bad, and has some graphics options that will stress my old card. MW3 has very limited graphics options, severely limited AA, and looks quite mediocre compared to the other games I have recently acquired.
-The changes from Skyrim-Oblivion > The Changes MW2-MW3. More innovation is better, as otherwise it is honestly just the exact same game with a bit of a reskin. Sure a few things in MW3 changed, but the resounding feedback from critics, and the players I know alike is that it was far too similar to MW2 and basically every other CoD game to be justifiably called a new game.
-Both games have glitches and problems, including lag issues, rendering them unplayable for some.
However, if you want a very flawed argument, as flawed as the 'Its more known, therefore its better' argument (Which if that's true, Mario is probably the best game of all time); Metacritic User Score.
However, neither game is actually better than the other. One may be a better choice then the other for a certain individual, but neither is better without a subject for them to be compared to.