[Mikord]

Honestly, if you really want to examine it, all of the current systems have their issues (downloads, ratings, favorites, addon spotlight).

I'll go over some below, but the main point is that none of them are perfect, and in the end there is not a compelling reason to get rid of any of them (except maybe downloads). The categories cater to different aspects and when all taken together help provide a fairly decent picture.

Downloads

Of all categories mentioned, this one is the worst. They are really quite pointless because a mod that is frequently updated due having dynamic data will naturally get more downloads as the result of large amount of updates versus another mod that is rarely updated because it is either customizable enough that changes are rarely necessary or the function it provides simply doesn't need to change much.


Ratings

You've already touched on some issues with ratings, and there is really no need to rehash them here. While they certainly have their share of issues, I find them to be better than the current alternatives. Users should have a method to show their appreciation for the quality and usefulness of a given mod.


Favorites

This is more of use to a user who wants to get notified of updates (or have quick access add the mod to the UI updater) as opposed to any kind of rating system. For those users who don't really care to stay on the bleeding edge, there is little incentive for them to make a mod a favorite.

This also indirectly suffers from the same issue as downloads in that mods that are more frequently updated due to dynamic data are far more likely to be marked as a favorite for the notifications of dynamic data updates versus one that doesn't need to be updated often.


Addon Spotlight

While this is a good feature, it is either random or subjective to the relatively minor number of people deciding on which mods should be in the spotlight. It has little, if any, bearing on what the user community as a whole thinks of a mod.