Some of the donation tiers bother me. Like one that lets players help create a challenge. There's 50 slots for this. I don't want fans designing the game. Then there's 50 slots to have "your voice in the ending theme". Why would you ruin the music like that? And you get to say what you want. I don't care what you have to say! OH! 50 slots for "your face in the game". 50! This totally impedes proper graphic design. The hell? 5 people get to help design an enemy. JUST LET THE CHARACTER DESIGNERS DO THEIR JOBS! I feel bad for the developers having to get assets from these people and find time to videoconference with them when they could instead just be making the damn game with their own assets and designs.
This crowd-funding stuff pisses me off. Their pledge levels definitely help get them money, but in my opinion they make the game much worse than it otherwise would have been without fans helping design the game and putting their faces and voices in it. I heard of some D&D-like thing where all of the characters ended up looking pretty similar... middle-aged white dudes with goatees because the makers had to make the characters look like the people who contributed. How lame is that?
I don't think it's going to be an issue for this game. Many of these are described in the Kickstarter itself and they don't sound at all like what you're insinuating.
"Create a challenge" just means give us an idea for an achievement, much like the 100 achievements in Mega Man 9. They said they would only consider challenges that are "within reason" and that there would be back and forth fleshing out of the concept between the team members and the backer. So in the end it'll just be an achievement and it won't be anything the team thinks is irresponsible.
For the "your voice in the game" tier, this is what they say: "With this reward, you’ll be contacted via email with detailed instructions on what to record and send back to us, so we can work it into the mix of that final credit-roll song." I can almost guarantee the voices will be part of a chorus chanting something. Think the final song in Space Channel 5.
And for the "your face in the game" bit, this is what they have posted: "Let’s be clear about this one up front: there’s a right way and a wrong way to implement this kind of reward. Our plan is to do it in such a way that you, the very generous backer who donates to this level, can take satisfaction in finding your mug (pixelized into a 2D representation by the game’s artists) and showing it off to your friends and family, without disrupting the experience for anyone else. (For example, one idea is to have little electric-poster displays in the background that show “Wanted” reward posters which cycle through these backers’ faces.)" So, again, it doesn't sound like this will hinder the game's design in any way.
As far as general design goes, Inafking wants the fans to be involved in the project. Don't forget Mega Man Legends 3 with it's open development and design community was his idea as well. Backers will get to vote on one design or the other and have influence over the game, but not any type of total creative control. Don't forget that Mega Man 2 through 8 incorporated fan designs both for enemies and for robot masters, and I love those games. It might be an issue in some projects but I don't think it will be here.