The only real argument Zappe had over Jones was that he looked more confident in the pocket. But that's not really saying much because by that point Mac had spent all year getting massacred. We saw what happened with Zappe. He got some breaks in his first few games (and one was a shutout), then by the end he reverted to as bad or worse than Mac.
Mac and Zappe's last games were both against New York teams (Mac was on the road, Zappe was at home in bad whether) and they both posted similar stat lines. Both had 0TD's, 2INT. Mac had 89 yards, Zappe had 88. Mac had a 27 passer rating and Zappe had a 20 passer rating.
If you compare where Mac was at the end to where Zappe started when he got the nod, sure Zappe was an "upgrade". But Zappe start was actually worse than Mac's start and Zappe's finish was virtually identical. Mac also had the overall best game. His Bills performances was better than Zappe's best performance and that's before you include that was the best team we actually beat on the year.
Zappe was sort of a case of "people saw what they wanted to see because they really wanted Mac to be the only problem".