I would go with 1
Although I make that "mistake" in spoken english, 2 erroneously says that the same temperature was same 15 years ago.
1 says that the temperature is now higher than the then temperature 15 years ago
Well Paul, my thinking was also exactly like yours. This question is from KAPLAN
and they have selected (2) as the correct one.
But in my opinion, both the choices are wrong. The correct choice should be
The average temparature now is two dgrees higher than the temperature
fifteen years ago
Choice 1 is I think obviously wrong because the use of "what" simply does not make sense.
Choice 2 is wrong for the reason you sighted.