I think it all comes down to personal taste. We LOVE the Contemporary for its energy... however, many people in the military have enough excitement and energy, and look forward to spending their vacations chilling out... and SoG has that type of atmosphere. I know that when my DB (who is an army officer) and his wife go to Disney, they are more interested in a laid back experience, where they can lie by the pool and relax. They don't want or need the energy or excitement.
SoG has very large rooms, possibly even larger than the Contemporary, and they have balconies, which North Wing rooms at the Contemporary don't have. Also, since it is run by the military, it is possible that there are other differences in how things are run, as well.
Convenience-wise, the Contemporary is more convenient, and the North wing is very nice.
Yes, when military stay at the Contemporary instead of SoG, they must pay taxes, as the Contemporary, although substituting for SoG, is not owned by the military and must charge taxes for all of their guests. But, yes, even with the 11% tax, the charges for staying there, if you normally would be staying at SoG,are far lower than anything anyone else would ever pay.
The Contemporary has the benefit of being on Bay Lake, which means that you may have the option of a Bay view... very beautiful!!! Also, to get to the MK, you need only walk. There are more dining options at the Contemporary.
SoG is on a golf course, and if you are into golf, that could be a nice feature. You can walk from SoG to the Poly and take the monorail from there to help with transportation.
As I mentioned before, it is a matter of personal taste. My parents loved SoG when it was the Disney Inn, but my taste goes more to the Contemporary, (Mickey's resort, as I like to call it)..so different strokes for different folks!