President-elect Trump didn't choose to comment on the salutation used by President Putin, as he called the letter "very nice."
I, personally, think it's important that we let president-elect Trump know that he was addressed incorrectly, and that how the President of the United States is addressed is important (just so nobody gets confused about what role a president plays in our democracy).
I'd like to think that president-elect Trump would let President Putin know that future communications should conform to the practices that our democracy has determined are proper, with respect to how we address the President. Salutations are important, and the way we do it reflects the kind of role we expect our President to play. Things may be different in Russia, but that's not the model we follow.
President Putin addressed president-elect Trump as "His Excellency."
At the time our nation was brought into existence, there was actually a very serious debate about the proper salutation to be used when addressing the President. The question was both debated and decided, long ago. "His Excellency" was rejected. The proper salutation is:
(Saying "Your Excellency" is intolerable, and it's just plain wrong)