Acrobat 4 format flattens all transparency. Acrobat 5 and 6 don't. Your export may be taking a long time because you have limited memory on your system relative to the amount of image that InDesign/Photoshop needs to process, or you're running out of swap space, or both. If you have several complex, multi-megabyte, multi-layered images on a page, with lots of transparency effects, then the export process can be very slow because all the flattening is being done at export time. Complex vector objects can also take a long time to render, particularly if transparency is involved.
If the later versions of Acrobat seem to “flatten the image too much,” I suspect the problem is with the color space, and it's the color changes that look like flattening. If you export Adobe RGB 1998 to CMYK SWOP v2, you might lost some of the colors of the RGB that can't be rendered in that CMYK color space. You can use InDesign's bulit-in soft proofing to get an idea of what the color will look like on press (View>Proof Colors) in the color space that you are exporting to. I don't know why the different PDF versions would give you different color renderings, though, unless you've changed the defaults for one and not the others. In that case, InDesign would have added “[modified]” to whatever PDF preset you were using.
When you do get a setting that works for you, I recommend you save it as a PDF preset so that you can use it again without having to set things by hand.
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