Part of the problem with QBs coming into the NFL now are the goofy offenses colleges are running these days.
In general, QBs are more pro-ready now than they ever have been in the past. And a lot of that is because these goofy offenses are filtering up. College coaches tend to be way less risk-averse than NFL coaches, and the result is that a bunch of different innovations get their shot, and the ones that work do filter up.
10 years ago, mobile QBs were more or less a gimmick, and now probably half of the starting QBs under age 30 in the NFL have the requisite athleticism and knowledge to run read option plays as needed. While the NFL's philosophical evolution has been driven by rule changes, the schematic ways in which teams go about making these changes have mostly filtered up from the college ranks. Look at all the work that Belichick has done with Urban Meyer for an example.
The real reason why quarterbacking is so all-over-the-map in college is because there just aren't that many good quarterbacks in the world. Look at it this way: there are exactly 64 starting + second string professional QB jobs in the world. Anyone who's a starter or a backup QB should, in theory, be one of the 64 best in the world at what he does. And yet Brandon Weeden and Blaine Gabbert are still among this group. That's how few genuinely good quarterbacks there are on the planet Earth, and that's when you're selecting out of the entire population over the age of 21 or so.
In college, there are more jobs to win, a much narrower range of potential QBs to select from (age restrictions), and they have years less of quarterbacking experience and coaching. So... yeah, as little depth as there is in the pro ranks, it's exponentially worse in college. There are
maybe 10 quarterbacks in all of the college ranks right now that will have any kind of a meaningful pro career. Not even necessarily a good career, in the sense that an NFL fan would define one. The rest just aren't good enough and/or haven't had/won't get the right coaching.
It's not a problem with the offenses - it's just a lack of available talent. It means that even the best programs in the country are frequently stuck with QBs who basically suck.