Note that the heading behavior in CKeditor is done on purpose to help non-technical users choose the right one. Since site heading is usually h1 and feature instance heading is usually h2 it is best for content in the editor to start with h3, so we have it mapped as h1 > h3, h2 > h4 and so on.
But if you don't agree with this behavior, you can change it by settings as shown in the arcticle Customizing the Editor Toolbars.
As far as alternatives did you know that you can edit at least blog posts and html articles using Windows Live Writer? It is a robust desktop application. See the articles:
Hope that helps,