I loathe giving any appearance of promoting my set; that just isn't my thing. But, I've tested a bunch of slider-based combos and what I am running right now (which is default with injuries at 10 in MM and 39 in CFM) has worked very well. I loved pure default but the same QB issues that you are elaborating on were driving me nuts. The injury slider (in conjunction with the fatigue and threshold) has a lot of locomotion-based effects and what I think has happened is that the 39 CFM injury value has gotten things back in-sync. The QBs are 'reading' the routes at the proper times and are thus looking at the downfield receivers at the proper times.
Sure, there are games with certain QBs where they throw short more (following their "ID") but overall, I've seen a lot of success with that setup (and people have reported good outcomes on both All Pro and All Madden). QBs with more aggressive traits will definitely throw downfield more...it keeps you guessing...a lot...which I really have enjoyed.