We REAAAALLLLY need to make a sticky post in this forum that very clearly tells people not to expect smooth playback of native files on their computer (I know this is touched on in one of them, but this needs to be in the thread title, so they'll read it). This is the most common thread topic that appears on this forum
The sum up: Everybody has totally crappy playback of native files, they're a nightmare to work with in anything but CS5, yada yada yada. As you said, after editing, the finished product is gorgeous, so it is what it is.
Bottom line, its not the 5D2 thats unworkable, its just the codec and how much resources it requires to play smoothly. I would rather deal with the headache of a native file that is gorgeous and practically unplayable than a native file that looks like crap and plays smoothly, but thats just me. I convert with Neoscene before attempting any editing. Will attest to its goodness, while working with CS4. As soon as I can afford it (or bosses at work approve purchase request), I'll upgrade to CS5 and say goodbye to the headache.
Don't mean to sound snarky, just so many threads on the same... thing... over... and over.