Can you define the "EP System" as you mean it?
Watson used the EP System in week 1 to pick apart a good New Orleans defense and last Sunday to demolish the Falcons. Hes used it in every good and bad game that he has had so far. By "EP System", I think you mean the "scheme". Peyton Manning and Tom Brady (and others...Chargers, Steelers, etc.) use(d) the EP System, but their schemes were not all that similar. Same with Andy Reid and Kubiak...both WCO, but the scheme is very different.
Watson operates the EP System just fine. Thats just the verbiage used to call plays. What I think you mean is that Watson has too many responsibilities at the line...which may be true...but thats because of OBriens scheme, not the EP System in general. Like ANY system, the EP can be as complex or simple as a coach wants to make it.
The scheme is/was overly complex for a young QB entering his 3rd year with only one non-rehabbing offseason under his belt.