In addition, it seems that you are going for the more "fair" system, but by setting a minimum NXT holding limit, aren't you excluding all those who have less than this amount? So small stakeholders are being disenfranchised even more so than the 1 NXT = 1 vote system.
Do you mean with 1 NXT:
1) 1 NXT in balance
or
2) 1 NXT fee
Either way. People with larger stakes will care more about what they vote on whether or not they have to pay for it.
I would say it is better to be based on 1 NXT = 1 vote (without pay), otherwise it will discourage voting. We want a large as possible agreement, so that means we want as much NXT in the system voting as possible.
Do you really think, it would discourage voting? Large stakeholders can't afford to pay high fees, just because.
Another argument should be counted in: large stakeholders do a lot to secure the system. So, why jeopardizing it via 'appearing unfair' voting? In a system where only the balance counts they have to create smaller accounts just to vote fairly (assuming they want because of the stakeholder-argument). When they can determine the voting power directly (via fees), I dont see a problem with that.
Paying fees has the side-effect that more NXTs are distributed. That's basically a good thing, I think.
The only issue I see with having to pay a fee is that people who care most (ie. they vote the most) will find that they have less and less voting power over time. Their NXT may flow to hoarders who never vote at all. Without a fee system (simply 1 NXT = 1 vote) then everyone is encouraged to vote as much as possible, on every topic. Of course, no one (especially large stakeholders) would vote for something that would harm their own stake, so there is already an incentive to vote for the overall good of NXT built in.