In FS2004, and in previous versions for that matter, a lot of the common animations were 'canned' so the developer could just call up a pre-made block of code and insert it where it was required. Custom code was only required for custom animations which were mostly gauges or non-common aircraft part animations.
In FSX all that changed and 'canned' code blocks were dropped and the developer was required to provide the required code.
This is why some port-over aircraft have issues in FSX as the 'canned' code blocks are ignored and thus the animations do not operate. In 'FSX native' aircraft the developer (or someone else doing the conversion) has taken the time to replace most of the important animations if not all of them.
Animation code was not the only thing affected either, prop blur code changed causing issues with clouds and trees in front of prop animations and transparency rules changes causing either missing windows or opaque windows. There are lots of other changes too.