I think with Russell Wilson we are witnessing quite possibly the most gifted point guard QB of all time.
To answer the OP's question you must first determine if you even like point guard QBs (as opposed to 'traditional' QBs), and that if you do, how much do Wilson's height drawbacks concern you?
We know that Pete covets point guard QBs. He was talking up such QBs long before he drafted Wilson.
The height drawback can be considerable at times, but I think the new quick strike offense Pete and Bevell have implemented the past three weeks has helped solve some of these issues. This progress was incredibly evident in the second half of the Rams game, but masked somewhat in the Panthers and Raiders games because (probably by coincidence) Wilson just didn't have it those days.
But even in the last two games where Wilson was way off on so many throws, he showed exciting progress as a pocket QB who could find open targets (including those over the middle) with Peyton Manning type alacrity. They've asked Wilson to play like a totally different QB, and he's taken to it very well, other than the small sample size issues with distance accuracy, which again is probably coincidental.
I have a very high opinion of Wilson. I love point guard QBs, who by the way are no strangers to Super Bowl Championships or even dynasty runs. Every thing Pete does is about winning, not about stats. Wilson is the epitome of a dream QB for Pete.
With regards to WIlson's issues, his work ethic (and Pete's) assure me that no problem he has will last forever. It's ironic, but Wilson has proven Mel Kiper exactly right, in that his greatness while overcoming struggles proves exactly how difficult it is to play QB in the NFL at 5'10" or 5'11".
It isn't showing in his numbers right now, but Wilson is a better QB today than he was in 2013, and in 2013 he was a better QB than 2012. Every few weeks you can see tangible signs of improvement in his game, and there is still so much left for him to unlock on his path to greatness. And he will unlock it. It is easy to be patient with such a QB when he's already won a SB, and is off to the best start of any QB in NFL history through 2.5 seasons.
I think it would be crazy to not pay Wilson. He is already the best under 30 QB in the game, unless you think Luck is better. In that case, Wilson is the second best. For roughly the same money as Romo, Dalton, Kaepernick, Flacco... this is a total no brainer. Even after signing a 20+ million a year deal, Wilson would remain one of the NFL's more valuable commodities.
Especially this year. With the struggles Seattle has had, there is no way the Hawks are 5-3 with an average QB.