So you appear to do everything right: you have a fair amount of unique content and you seem to update your site regularly and Google seems to often visit your site… but there appear to be much fewer links in Google’s index than there are actually on your site.
So what may that mean?
1. Are there really few pages in Google’s index?
You might be wrong about how many URLs are actually in the index as there appears to be no definitive way to tell this. SITE: command may be inaccurate and Google Webmaster Tools reports may be unreliable.
! To make sure a URL isn’t really indexed, use your traffic analytics tool to see if there are no Google search referrals to this page. If the page is ranked, there should be nothing wrong with it.
2. Evaluate your content quality
Google may keep visiting but failing to find pages useful enough to store them in the index. By “useful” content I mean unique text content longer than one or two sentences.
3. This may be just seasonal / temporal
We’ve discussed this before and here’s a helpful forum thread about that: during some (“busy”) periods of the year Google may hold off indexing new URLs:
…the “holiday search results” you know. While Google is in this mode (at least what we’ve seen in the past) the basic spidering, especially for young websites, continues but their indexing is often in a holding pattern.
4. Your site is too young: wait a bit
Google treats new sites with suspicion. It doesn’t want to store data of the sites it doesn’t trust (or it may be storing the URLs already but not telling you to watch the trend). So just keep adding quality and relax.
5. Check for some stupid mistakes
I’ve seen quite a few people coming to me for SEO diagnostics complaining of bad indexing rate and having Noindex meta tag all over the place.
Looking back at the post, I can’t help noticing that there’s only one “true” issue listed (the content quality) – 2 of five points describe a perfectly normal situation and one is about improper diagnostics. So is bad indexing really not an issue most of the time?
Sadly, it is often an issue. But to diagnose it, you’ll need more information: like cache rate of your site pages, possible Webmaster Tools errors, low rankings, etc. Like I said, the indexing rate is too hard to diagnose to signal of anything…