Amendola still averaged 4.5 catches per game in his horrible season, had a much higher 1st down rate than Edelman, had a bigger YPC average, and caught 2/3rds of his targets. Had he not missed those 4 games (it's hard to argue, I realize) he'd have caught 72 passes this year. While that's not "great," it's not horrible enough that we need to question his chemistry with Brady in his very first season here.
Maybe you don't remember the preseason game where Brady hit him 7 times in the first quarter and everyone here was excited as hell? That didn't look to be anything of a chemistry issue to me, neither did the first game of the regular season.
The issue was that Amendola became injured, and Edelman received 151 targets compared to Amendola's 83.
Even if you're correct and there is a chemistry issue, I doubt that it's anything to be that concerned about after a whole new offseason of OTAs, minis, TC, and the preseason.