The key does not avoid pagination, but does not rely on pagination. When you rely on it to display large lists of content, you apply this "many click" navigation. You want the user (and therefore robots) to have simpler and more intuitive ways to access your content.
Usually, when you look at pagination, you are at point IA, which is not easily broken into a hierarchical structure. At this point, the best approach to get a lot of content is through filtering using tags.
Take SO as a good example that essentially has no IA behind a large gigantic list of questions. On the main page of questions now there are 142414 pages. If this were the only way to find relevant content, it would be NIGHT. But a good tag system suddenly makes it easier to use. For the sake of simplicity, pretend that paginator has only prev and next, and there is only one sort order, in fact, these functions help improve the depth of questions in a similar way, giving shortcuts through the list, but not where near as much as tags.
As soon as you click on a tag, you will get links that add related tags. You can narrow your questions very quickly. Think about going to a question somewhere in the middle, did I choose RSA blind signature using the .NET cryptographic API? which was on page 70,000.
It takes 70,000 clicks to get normally, this is obviously very poor SEO. On the Tags page (1 click) “Encryption” on page 6 (6 clicks) add in “Cryptography” (7 clicks) add “rsa” (8 clicks) and in “.net” (9 clicks), and the question appears on the page . Moving there went from a depth of 70,000 to 10. Without the assumptions that I made earlier (skipping pages and using different types), there are likely to come across several more places.
Add to some other basic SEOs such as meaningful URLs, meaningful headlines, keywords in headings, and you're pretty much there.