Two of the more common problems likely to be encountered when using the MicrosoftEolasFilter, particularly with Flash, are attribute quoting and tag closure. It would be a bit of a stretch to say that these are the only problems you are likely to encounter but this will give you a good head start in coping with the spectrum of possibilities.
Attribute Quoting: One of the more common oversights in writing well formed HTML, is the lack of quotes around attribute values. The browser never complains of this and designers and users never observe this condition unless the value being assigned to an attribute is a string of characters containing a space. This is a violation of the well-formed rules of XML and will cause problems with some XSLT processors.
Tag Closure: Singular tags that contain no body content or subordinate tags should be closed with a forward slash before the closing angle bracket. For example:
<param name="some" value="thing">
<param name="some" value="thing"/>
Intellectual patents have always been a double-edged sword, and their close cousin the software patent is not any different. The tragedy of patent legal entanglements is that they often create more work for the already overworked. Microsoft's proposed workaround, while probably a real legal technicality that might stick (though to be sure there are people combing that one over carefully), still requires developers using their technologies, by choice or not, to manually clean things up just to keep up the status quo.
While this solution is not wholly without a manual component, it is one that requires less work and doesn't require the application developer to change his or her current course of work. Further, it should take significantly less time to make changes to one XSL script then to rewrite all instances of the active content in HTML.