I haven't found a way to sort the mods in a given category by rating/downloads/favorites. It seems like they're just sorted by recent with no way to change this, either in-game or on bethesda.net. This makes it virtually impossible to search for mods unless you already know the name.

To make matters worse, the automatic "Most Popular" and "Highest Rated" categories only show about 20 entries and on console there is no way to continue past these 20. This makes every mod except the top 20 completely invisible to users.

I was optimistic about Bethesda.net, since it was incorporated completely into the game. But with these drawbacks it doesn't really seem usable.