What he means is that the way that Madden handles passing is flawed and hurts not only the offense but the defense.
He wants route based passing where the thrown pass is based on the route and timing to a greater extent. How Madden does it, is that allows you to be successful, sometimes unsuccessful, by having the thrown pass based off of the direction the receiver is going for the most part. What is the point of having patterns then?
If the WR is running an out, but the QB is pressured and throws it early, the QB should still throw the pass outside to where he thinks the WR should be given the route. So if if the WR hasn't broken yet, the pass will be thrown towards the sideline, where it will fall incomplete or the WR may be able to just get to it or it could be intercepted. In Madden, in this scenario, the ball would be thrown like it's a Go, because the WR is still running straight up the field. If the first example ends in an INT, that's Football. If the second one does, that's the game causing it, not you. And this goes for the D as well. If you were to complete that improvised Go route, it makes it hard to play D when you do everything right, and get pressure, but it doesn't matter because no matter what, the QB will almost always throw the ball where the WR can catch it, whether it was how the play was drawn up or not.
It may not seem like a huge issue, but this is why there are few passes that ever hit the ground in Madden or sail out of bounds. Just about everything is a catch, drop, pass defense, or INT, but hardly bad throws.
You might think that you can throw timing passes in Madden, but you really can't. The window to do so is so small that if there is some kind of double move in the route, the direction he was going at the time you pass is the direction that the pass will go, regardless of whether there are more moves after wards. This happens the overwhelming majority of the time. There are patterns that are exceptions to a certain extent like hooks, but those are basically straight line routes any way so not much difference when you release it.
Precision passing is also an illusion. The AI is much more in control of where the pass will end up then what direction you are holding the stick. Don't believe me? Throw a crossing route and hold the stick in the direction that would make the pass be behind the receiver. Hold it in that direction for a long time prior to try and throw the pass so far behind that it falls incomplete. Or even so far in front that it falls incomplete. The majority of the time the pass will still be on target. If I can't even purposely throw behind someone with precision passing, how can I call it anything other than an illusion? With route based passing, this would never happen because if I was pressured and threw it too early, then it would be overthrown because the pass is tied to the route and not the receiver. Conversely, if I held it too long, the pass would be behind the receiver. Now I'm not saying that the QB shouldn't be able to make an adjustment, but that is where the precision pass should come in. To try and correct for errors in timing and coverage, but if the ball is gonna go to the receiver anyway and towards the direction he is running for the most part, then that makes for a bad passing game mechanic for both the O and the D in my opinion and makes precision passing useless.
This is what I think that Valdarez meant. Obviously every bad play is not the game's fault, but there is a definite framework built into the game that makes it very hard to not make mistakes, regardless of your Football acumen.