I don’t think that you will see many problems when using HTML AIR mode, AIR uses the Webkit engine under iirc covers, which can work quite well and has most of the same built-in Flash / Flex functions of built applications. You will also see most of the HTML5 features you will find in Safari. I would say if you need animations in which Flash will usually work better than Canvas at the moment ... There are many examples of ExtJS and other frameworks that work in AIR.
As for the fact that you refuse, I do not think that you will lose anything from HTML to HTML / AIR. You could get a lot of what you get from the fact that the whole application is based on Flash on top of direct HTML. In flex, custom controls and other features can be more easily customized than standard HTML controls. Flash animation tools are much nicer. ActionScript does not conform to JS based on one, so code problems may occur. Working with remote content / data is actually a little better imho in AS compared to XHR, but only when working with XML.
From an administrative point of view, switching to AIR using HTML from an already written application is probably the shortest way. If you really need to, you can convert later and a lot of logic will be developed. Time to market will be shorter with the one closest to what you already use most often.
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