jwilburn To answer some of your questions:
How often do people purchase web games? I never have. I don't know anyone who has.
It's not a common thing at all right now, but that's mostly because there was never an 'app store' for web games in the past - people are used to them being free. The more common model is definitely in-app purchases, but you already said that won't work for your games, and I understand.
To make $1-$5 games more of a norm (like it is on mobile devices) the process has to be dead-simple (similar to Amazon's 1-click checkout...which is patented, so we can't get that simple). If I had to go through a four step process, or even have to deal with going through PayPal for a $1 game, I'm a lot less likely to purchase it. This is where we can come in and provide as close to a 1-click experience as possible (without violating the patent) for Credit/Debit card transactions to hopefully make paid games a bit more common.
Say I just created a new game and put it on Clay.io. How much exposure is my game getting? How does that compare to Chrome Store? What's the benefit for me as a developer to sell through Clay.io over Chrome Store? when Chrome Store is likely getting 100x the exposure for my games?
The Chrome Web store certainly has more exposure overall - if they feature your game at the top of their store, it will get more downloads/purchases than if we were to do that no doubt (at this point in time). However, according to this there are 44,000+ apps, so a lot of games aren't going to be noticed much.
The exposure on Clay.io is more targeted (people actually looking for games) and not as diluted (far fewer games available to play). Of course, we are still growing to, and are putting a lot of effort into the growth of the site.
You're not restricted to selling your game in *just* Clay.io, or *just* the Chrome Web Store. Feel free to put it up in both.
How do I secure my web game? What's to keep people from stealing the code / assets and re-releasing it with a few tweaks?
The obfuscation and minification is enough to halt that some (they'll be able to un-minify, but all the variable names won't make sense, there won't be comments, etc). The big thing is having a backend for your game. They won't be able to steal that, thus the code won't be complete. The same can be done for Flash games, but I haven't seen any blatant copies of, say, Farmville tossed up on somewhere.
I think it's probably a bit unrealistic to expect my situation to be unique considering the amount of discussion on this site regarding CocoonJS, Awesomium, and other export options.
What I think would be unique is the fact that you're not planning on a web release of your game at all (which I do understand in your case).
As for the rest of your comments, I'll keep it in mind and discuss it with my co-founder and advisory board but like I said before, I'm not a big fan of a model where developers have to pay for 'features' even if there game isn't successful. There are other means of revenue down the line like an Ad API or charging for premier placement in the store.
Zanuff - $0 items can't be purchased, so that error message should show, but the other text (awaiting response from paypal) shouldn't have been. That's fixed. The API has just been tested by myself - it's not currently used in any of our games, so there might still be some bugs here and there. If you find any, let me know and I will get them resolved ASAP.