The answer to this issue is quite simple, in my opinion, and the answer originates from psychology.
The preference for Luck over Wilson begins (though doesn't end) with three major principles: Confirmation bias, the backfire effect, and the Ben Franklin effect. The confirmation bias, I think is obvious, especially when dealing with non-Seahawks fans. They "know" Luck is better, so they look for reasons to justify their position. (This is troubling when it happens with Seahawk fans who would still take Luck, despite everything they've seen with their own eyes.)
They have taken their position because of the Ben Franklin effect - which states that you come up with the reason behind your feelings after you've taken action, not vice versa. In this case, analysts and the casual fan have spent so long praising Andrew Luck, declaring him the next Peyton Manning, that they have no choice but to psychologically assume he's the best. Their action begets their feelings. In the opposite end, they've spent so long maligning "game manager" Russell Wilson, all they can feel towards him is disdain, at best.
The backfire effect then deals with the fact people will not only ignore facts that contradict their position, but they will, in fact, dig into their conclusions even further. So whenever you present the multitude of accomplishments Wilson has (that Luck doesn't), you're actually losing the war.
Finally, there is a very simple reason GMs will not outwardly praise Wilson, and it's job security. The only man who can publicly enjoy Wilson's success is Schneider. If any one else were to say that Wilson is better than Luck, the first question they'll receive in response is: Why didn't you draft him? Even a successful GM will have that blackmark on his resume when his team takes a nose dive to mediocrity (or worse.) (Whereas as Pete and Jon played chicken with the NFL and won.) So they have to publicly decry Russell, else they fall under scrutiny. They, after all, had no choice but to 'pass' on Luck, since they had no chance to draft him in the first place.
This is why the players voted Wilson higher. They will not feel the same scourge on their backs.
We all know Wilson has accomplished more and accordingly deserved the MVP talk during the middle of last season. He will continue to play at a high level and prove people wrong, while Luck maintains his current career trajectory more in the line of Peyton Manning (1 ring) or Dan Marino (well, you know). That's fine by me.