I think that these are 2 separate questions. One question is who should get HOTY and the other is who will probably get HOTY. The answer to the 1st question is Accelerate. The answer to the 2nd is Justify. Winning the TC usually earns a horse HOTY but not necessarily. Omaha did not get HOTY when he won the TC. that honor went to Discovery.
Yes Justify did dominate the 3YO crop during his brief career but never beat or even faced open competition. How he would have fared against Accelerate who has proven himself against all comers, including an impressive BC Classic win, is a matter of speculation. However Justify will probably get HOTY because most non-racing fans never even think of racing beyond the Kentucky Derby or Triple Crown 1 day or 5 weeks a year, so they will probably pander to the ignorant masses and give it to Justify.