Hi,

Did you check your robots.txt? Make sure that it's not blocking any urls on your sites.

Are any of your webpages containing duplicate content? Google will filter out webpages that they find have duplicates elsewhere on the web. You can buy some credits and run a bulk check on Copyscape.com.

If these are not the issue, you'll need to:

(a) create more internal links within your site to help Google crawl your site. Deep internal pages are usually hard to find. Start with the more important pages on your site, by linking to the important pages from your top indexed pages or from the homepage. If you are using a wordpress site, use a plugin like SEO Smart links to automatically create internal links throughout your site easily. Make sure you variate the anchor texts to the same webpage though, to prevent over-optimization.

(b) use services like ping-o-matic and indexer services to get your pages indexed faster.

(c) wait patiently. BTW, not all pages will ever show up on your GWT report, but it shouldn't be that low a percentage.

Hope this helps!

Regards,
Jinghong Chiu

Submit a sitemap and ping the urls which are not indexed yet.

Do you target keywords to all of these pages? Do they ave content on them? Start more internal and external links to the pages you want to rank. This will help.