Called route trees had just been introduced with Gilbert.
Dino loves option routes. It is why you see so many badly thrown incompletions, QB and WR are seeing different things and WR is running a different route then the QB expects. The 3-3-5 defense has become significantly more popular due to the advent of the spread offense and, I believe, has made the option routes harder for both sides to read. The "Baylor" offense hasn't really seen a lot of success lately and those teams that have won, have won via their defenses.
As to why Syracuse WR's aren't very good. A lot of misses in recruiting. Courtney Jackson is the best WR on the current Cuse roster, but was being underutilized before Taj left (he was the guy we were hearing about in the preseason). Misses on the outside WR's have been a problem and they are compounded by the fact Syracuse runs a ton of option routes, so it takes longer to get the talented freshman on the field. The crop of freshman (Alford, Pena, Hatcher, Gadsden) has as much potential as we have had in the WR room in the Babers tenure. They are just young.
I think eliminating option routes, having an actual playbook and having WR's just learn the nuances of route running and getting off of press coverage would help to miminize their learning curve and get the most talented dudes on the field. Problem is, S. Johnson and Queeley are your best blocking WR's.