Part of my problem with the fees - and I think they're a bad idea even if not as vehemently as Dave - is that you've created another broad category of stakeholders, one I don't think you really want: Losing Players. A lot of your core design rhetoric has been based out of the idea that there are no losers, that the game is stake-to-play rather than pay-to-play, and until now that's been at least believable.
But adding tournament fees, regardless of where they go and how much overlay you offer, is inevitably going to create players who continually lose money. That's another group to keep happy on top of the eleven you've listed, and one that's generally hard to find synergies with the others. That's going to end up far more of a headache than not having "too many" people in a freeroll would ever be worth.
(I'm just waiting for the first major "Monsters is rigged" theory at this point. That's not going to be fun. They don't go away. Everyone's going to feel like they don't retaliate often enough, or their same-speed cards don't go first often enough, etc. And evidence doesn't matter. That hasn't mattered when losses aren't meaningful, but it's sure going to now.)
Also, as someone who makes money from people buying cartoon fantasy creatures and having them attack each other, telling people you don't want them to be frivolous is pretty much shooting yourself in the foot. The whole game is frivolous.
We already have the losing players group. I am in that group and been waiting for auto tournaments and/or card prices/sales to pick up to pull me out of it. I am accompanied by many others in the same situation but that's the nature of the game.
I been warning about the, " this is rigged" topics likely to start for awhile. As you pointed out, once they start it will snow ball into something that is uncontrollable and no amount of proof that it isn't rigged will stop the discussion of it. I don't think having buy in games is an issue as long as we are still getting the $100 daily / $1000 weekly freerolls promised. I actually think buy in games to accompany the freerolls is a great idea and helps to replenish the funds that are put aside for creating more games.