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I have just recently begun to use this technique with some smaller sites. I design the page so that the popup window only allows the enlarged image to be visible and the window is not scrollable. However the visitor who comes directly to the URL from a search engine will see a full "proper" page, complete with links back into the main site.
Pop-up pages can offer a good opportunity for SEO, especially on sites with low total page count or text-poor pages. For instance, I have several artists who want essentially non-verbal sites. Each optimized popup page can become a well focused doorway/hallway page.
I've only done a little bit of this to date, but so far the results are very promising.
You certainly could optimize for more basic keywords. By doing this you're adding to total page count for the site, giving the SEs more on-theme text and more in-site links. All that can really boost rank and traffic.
One thing though - cranking through the production of 2000 pages might lead you to fall into lots of repetition, and you'll have what looks like duplicate content to the search engines. That can hurt. (I've done this!)
You might want to start with pop-up pages that offer an opportunity for the best, most on theme, subject matter. In other words, see what you can achieve on a smaller scale first instead of doing all 2000 pages and then having to make massive changes.