To what format are you exporting? Sounds like you are using unfavorable combinations of some features and saving to an older file format version.
i'm exporting from illustrator cs 2 as a psd and opening the psd with cs3 photoshop
what features can i try to change for a better result?
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Well, without seeing the document that is impossible to tell. However, there are a few standard cases that would cause layers to be flattened.
- nested transparencies and blending modes inside clipping masks
- knockout groups
- multiple gradient meshes on top of each other
There are a few more, but that should give you a place to start. Basically you should look, whether everything you do is organized in as clean a manner as possible, i.e. on layers and sub-layers with only one level of grouping. Also, in case of symbols, expand everything before exporting (Object --> Expand).