I had over 3,000 pages in the supplemental index.
Contrary to what a lot of people say, being stuck in the supplemental index is not a penalty (although it could be considered a type of filter). Regardless, though, its not a good thing.
Being stuck in the supplemental index simply means that Google does not consider your site important enough to put in their primary index. This could be for several reasons:
1. Maybe your site isn't worthy of the regular index
2. You don't have enough inbound links to your site
3. Google is confused by your site, causing pages to appear unimportant that really are important
That list is not comprehensive.
You should do a full analysis of your site from an SEO standpoint. Look at your navigation first (this is one of the most common fallpoints into supplemental, IMO), check to see if you have duplicate pages (you can have dups without even trying), and, most importantly, figure out who is linking to and whether or not those pages linking to you are important.
For the record, I've gotten sites out of the supplemental index in two weeks, and some sites out of supplemental after 1+ year. It really depends on the size of your site, what's wrong, and how quickly you can make changes.
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