I would think that no more then one in ten million would be concerned with not being able to change the default Windows font without being able to make a registry change and I might be under-estimating the odds. I'm not judging you or your concern, because that is what makes you unique... But think about this for a minute... how many people out there would even think to change the default Windows font and then how many of those that would care that a registry change be required to do so. I can do everything I need to do and was pleased to see that without Aero, I can now set the font sizes on individual items, when I couldn't do it before in WIN7 Aero, without performing a wholesale enlargement of all fonts, bringing many apps to their knees.
As far as the charms and clock poppiing up, if you disable the active corners in Classicshell, that will stop. I am with you on using third party apps, but Classicshell hasn't caused me any problems yet and it sure makes me happy except for the slowness of the Start Menu popping up.