I think that Zay would have really benefited from a Sammy Watkins type presence at the receiver position. That's not to say that I don't think that the Sammy trade was good but rather that the offense not having a true number 1 receiving option could be impacting his ability to get good matchups.
Jordan Matthews is a nice player but he isn't a number one receiver, Charles Clay is a solid tight end but he isn't a dominating presence like Gronk or Kelce, and they don't have another high end receiving option out there. So Zay is going to see a lot of high end coverage coming his way. That's going to result is less production and it could be impacting his confidence.
I think Zay figures it out and I also think that the coaching staff finds a way to get him involved and get his confidence going. Although I don't think any receiver or tight end puts up monster numbers on this offense, simply because the defense will likely be good enough to keep them in most games and the rush attack will be the most effective way to move the ball. Also the offense will be low risk in general to avoid turnovers.
I agree with you that currently that the Bills don't have a #1 receiver. And I agree with you not having that caliber of receiver does impact Jay Zones as far as not opening up the field for the secondary receivers. As you suggested there is no point in re-litigating that trade. (Even acknowledging Watkins's dynamic talents I understand why the deal was made.)
As others have stated I think that once Jones makes some catches he will play with more confidence. In college Zay Jones was a high volume receiver. I'm sure that the more he plays and he will become much more dependable as a receiver. I'm confident that when the season is finished our top three picks will turn out to be good picks, especially our first pick who I think is a gem.