I think when they say system QBs, they're talking about how particular colleges rely on the shotgun or unusual formations that you don't see in the NFL, and that these formations will generally be pass-friendly and kind to his numbers, making the prospect look a lot better on paper and in the field than he will in the NFL.
Like, look at Hawaii. They run out of a shotgun every single play, with zero running game. That makes Brennan's numbers great, making him a system QB.
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