I can understand "messy" but in this way:
In final cut pro legacy (or other NLEs) you put clips wherever you want, in whatever track, and they stay there and don't move. However, there is no relationship between clips. The timeline doesn't distinguish between SFX or B-Roll or whatever. All clips are independent. They are all independent (with the exception of an audio track linked to a video clip). Therefore relationships were kept in the head of the editor.
FCP X is all about relationships. Relationships between clips are now the norm and are a part of the timeline itself. The timeline "knows" what is B-Roll over an interview and knows what is a SFX on a car crash because of the relationships.
FCP X gets messy when we want to take back all the relationships in our head. Then we are fighting with the magnetic timeline rather than it doing our biding.
I think you'll find that if you take the time to learn how to wield the magnetic timeline you'll find that it is brilliantly thought out, efficient and allows your work to be done much faster than a track based NLE. But really it is a matter of preference, I can totally understand why someone wouldn't like it and think it is messy. But I find that it changes the editing process and frees your mind to focus on the edits themselves rather than how to wield all those clips. I feel that it makes me a better editor because of it.
Now there are times when the relationships can drive you crazy (specifically in doing multilayer composting ) in the timeline and you want to just place items. You do need a workaround for this such as secondary story lines and other tricks, but those workarounds are nothing compared to the typical workarounds that are needed in track based NLEs.
You might have seen this videos before from Apple, but you might want to give them another viewing. They are quick and a little marketing heavy but they are very true.
http://support.apple.com/kb/VI288
http://www.apple.com/finalcutpro/includes/videos/overview-faster.html#video...
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T. Payton
OneCreative, Albuquerque