Do you primarily use 21 or 12 personnel? I used to be a big 21 guy four or five years ago, but I've gradually moved towards 12 and 11 as my two primary groups.
Regardless, my absolute favorite way of attacking Cover 3 is using variations of the Dagger concept.
That's one of the traditional ways of running it, but what I've done in NCAA 13/14 (haven't played Madden in years, although I'll probably buy the PS4 version when it comes out) is recreate the concept with the #1 (widest outside) receiver running some kind of post, preferably where he stems inside initially (unbumpable vs. man coverage). I'll do it from both dropback and PA, but I've found that PA is ridiculously consistent for me (I probably average 85% completion for at least 20 yards a pop). Really, all I need for this concept to work is a play where the #1 WR to one side runs a stem post while the #1 to the other runs a stem dig. So think plays like "PA WR In" from I Form as an example.
Basic "rules" and how I run it:
3X1
#1: Post
#2: Flat
#3: Go
Backside I always have a Dig route of some sort that will get in my vision should the post not be open. If I'm in empty, I put #2 on the weakside on a drag.
2X2
#1: Post
#2: Go
#3: Swing
Backside I block my TE (if it's 11 or 12 people). If it's a WR, I drag him like empty so that he comes open before the dig.
2X1
#1: Post
#2 Go
#3 Flat
Regardless of how I line up, I read it top down. First look is always to peak the Go route as an alert: while I rarely throw to him, there are occasions where a user plays unsound defense and he's open.
My second look is the post route. What I've found is that play action from under center will help suck up the underneath coverage linebackers and create a huge void for him to come open against either Cover 3 or 4. Hell, even if there's no play action he's usually open because hook zones usually stop covering people after about 12-14 yards or so. The idea is to hit him a couple of steps once he breaks to the post, a lot like the old Rams Martz teams use to do when throwing the deep dig off a speed cut.
Third look is the dig. As you scan your eyes to the post, if he's covered it's likely that a middle hook zone defender managed to get great depth. If that's the case, the dig should come open into that void.
Last look is the checkdown, whether it's a drag or the flat route (usually throw this when someone plays really soft Cover 4 and basically concedes that area of the field).
The main idea of this concept is to run off the FS with the Go route by a slot receiver: that will prevent him from driving on the post that the CB will usually pass off. From there, it's almost like a pyramid style read, working from the top (post) to the middle (dig) to down underneath.
Now, if Madden's actually improved their zone logic significantly than you may have to tweak this concept a little bit.`One way to do that is to line up in either a 3X1 set of some kind or 2X1 two back: in either case you want a WR/TE/FB to run an option route/hook to control the strongside hook/curl defender's drop. Odds are that guy will bite on said route most of the time, giving you a clear window to drill the post route for big yardage.
Offensively I run maybe ten total concepts in the passing game each time a new game comes out. Each year certain routes will be more effective than others: I tweak what I do based on that. For instance, in NCAA 12 short in routes were excellent against man: as a result I made Levels a staple of my offense. That hasn't been true recently, so I run more Smash (great vs man to man and easy to read period) as an example. The bottom line though is that I won't run a play/concept if I don't have a defined answer for man coverage and pressure defenses.