I hate to sound like a broken record, but there are so many posts in this thread that also sound like broken records...
Complaining that a tools is the BEST TOOL TO DO X ever, then bashing it because it is designed for platform Y is similar to making this argument:
My coffee maker is the best coffee maker I've ever seen! It's so easy to use and it makes the best coffee I've ever tasted. I just wish it would make carbonated beverages. I love my caffeine to be in soda format, but all my coffee maker will make is coffee which I don't like the taste of...why can't Gevalia change my coffee maker to make soda instead? It would taste better and everyone would buy it!
The bottom line is, C2 is a HTML5 based engine. That's all Scirra is responsible for.
Here's an idea: You want native code, write a native exporter. C2 can be written to do this. You want Scirra to do that for you, but it doesn't fall into their plan. I want an awesome survival game like Unreal World, only with a lot of added features to it...but those features don't fall in line with Sami's vision for his game...however he has added in mod support. I can either praise him for his great game, then bash him for not doing things the way I want, or I could write mods that add in what I want in the game.
Actually, I decided on option 3: Write my own game, but then again I'm crazy like that.
The point I'm trying to make, again, is that C2 is and IDE for HTML5. If you don't like the HTML5 platform, you're on the wrong IDE even if you think it's the best IDE out there. If you don't like what it exports, write an exporter or if you don't know how to do that and have a bunch of money find someone who does and throw cash at them to do it.