In my opinion, the stats that made everyone hate him, were a result of his abysmal supporting cast at Wyoming. Most small, untalented schools, play other untalented schools, so stats are still relevant. Wyoming was playing out of their class. They had no talent, especially on offense (minus Allen of course). The interior oline was among the worst I have seen.
Plus he played in a pro-style offense, so his stats suffered from that as well. Modern college offense lends itself to better stats, especially completion percentage. Another factor of playing at Wyoming...
The stats guys hated Allen. The eyeball guys loved him. I'm with the later.
If Allen played with better talent he would have went #1.