SK is the best. SR sounds nothing like Skyrim, and the 'R' sound isn't pungent enough to make a good abbreviation. DF, MW, OB. The second letter is always stronger than the first. SK follows in line with that, SR does not.
I think it has more to do with the number of syllables it represents. For instance, following "SK" we would have "DA," "MO," and "OB" for Daggerfall, Morrowind, and Oblivion. Both work for Oblivion. because the first letter forms a strong syllable on it's own.
So in short, I vote SR. SkyRim.