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One of our quandries is thinking "so many big companies use Omniture, they can't all be losing this much data, can they?" but I don't know how many people are comparing their omniture data to other sources, and I also don't know how likely we'd be to hear about big problems big companies are having with it. Also, I don't know how many companies are in the position we are to see that implementations for at least half a dozen different website consistently show problems.
We use Omniture and while I definitely agree its not the same as some of our other sources, it's usually close.
As soon as Data Warehouse releases a custom report, I plan to compare transaction to transaction against the report that our paid search guys give us. After that, maybe I'll be able to give you a better answer.