The 500k unique limit in Site Catalyst and Discover is hampering your product. Having to attempt to work around this issue put unnecessary complexities into your product. Discover did not use to have this problem, but recently it has.
Increase or get rid of this limit altogether.
For some of the issues. A big problem is that if a very popular page occurs at the end of the month (or after the 500k has been reached), it doesn't show up as a popular page.
A problem this does not resolve is looking for a specific UR, for example, that may or may not be popular, but is still important. For example, I want to find all URLs that have a certain s.prop value that is incorrect. I can't find these now as they are typically in the uniques exceeded bucket.
Well, if it's a choice between having all of the uniques or just the top 500k uniques without any other consequences, then I would take "all" unique.
If Site Catalyst slows to a crawl and you can't get data back because of the number of uniques, then I would take the top 500k.
What I don't want is what you have today -- first 500k unique.