WOW, this is an interesting thread. In theory, rel next prev is what Google wants you to go with. In practice, however, I haven't not seen this work as advertised by Google, and end up going to rel canonical in most cases. Here's one way to think about it:
Allow non-filtered pagination for top-level categories to be followed, but NOT indexed. Give them their own rel canonicals (self referencing) and ensure the intro content (or any other static content on the page) only shows on the first page (which should rel canonical to / instead of /?page=1). This will ensure your product pages all have a path going to them. Use rel next prev here, which "may" help the main/first page rank better by consolidating ranking signals from the paginated set.
For sub-categories and/or filters/facets use rel canonical pointing to the canonical version of that category page.
None of this, however, takes care of the crawl budget issue on enterprise eCommerce sites with crawlable filtered URLs. Therefore, I also use the robot.txt file, or nofollow attributes in links to handle this. I don't often use the nofollow robots meta tag for a variety of reasons.
Again, in the real world rel next/prev doesn't seem to be working very well. I haven't tried it in awhile, but it just doesn't seem to do what Google says it's supposed to do. This is why you see a lot of sites using rel canonical instead. I think we should think about this in terms of where you are in the architecture instead of trying to fit all pages into a single scheme. For example, some sites may even want to allow the first facet/filter to be indexable - such as "Filter by Brand" - because people are searching for it. If that's the case, I'll often advise they turn that into a real category instead of a filter. Another example, if you sell kitchenware and Pots & Pans is a category but Material is a filter you're missing out on a lot of searches for things like "Copper Pots & Pans" or "Stainless Steel Pans". It all depends on the situation, and has to be evaluated on a case-by-case basis.