I'm a pretty big Allen fan and I actually think he's knocking on the door of being a top 10 QB now. However he wasn't an accurate passer coming into the league.
In college I think he was an accurate thrower of a football, but not an accurate passer. Of course his support cast and the offense he played in didn't help his completion percentage, but even watching the tape, for every bullet he zipped into his receiver's hands, he airmailed a ball or missed on a bubble screen. I mean It's one thing to be able to stand in the middle of a field with no-one around you and hit a bullseye from 25 yards away, but it's another to do it in game conditions. The whole "looks good in shorts" took off as a joke, but this is what they meant by it.
Now these misses didn't really make sense when watching him throw because his mechanics, at least from a upper body standpoint, were near flawless. He's got a quick and tight release with a rocket arm. To people that haven't watched him actually throw, he's as good as the Rodgers' and Mahomes' of the league in that respect. Then compare it to other guys like Tebow and Bortles who have broken mechanics with long-*** windups which lead them to spray the ball everywhere. That's who you'd expect to have a mid-50s completion percentage.
So It's pretty clear his problem was timing and footwork. Wyoming, no offense to them, I'm sure don't have a great staff, at least not nearly at the level one would expect in the NFL. So it's not a surprise that after having spent over a year training with NFL level coaches, he's ironed out some of the issues and his completion percentage is flying up. He's rapidly becoming an accurate "passer" and I'm confident that in a year or two, will be among the elites especially considering his value as a runner.