I find it very hard to find certain mods I am looking for, especially when I am trying to figure out whether or not I have conflicting mods on (like two Mods that Modify Riften.) I had this great Idea that I would take all the mods I have downloaded, write them all down in classifications (like all the mods I have that Modify NPC's would be under NPC's) and then open them all in the CK and save them all in one big mod, thus making it MUCH easier for me to find the mods that I want. One of the biggest things it would do would be to compile all the different "armor" mods that add craftable armor to the game, thus only having to select 1 mod in my Interface for whatever number of Armor mods I downloaded. I realized, though, that a big problem lies with this. If I were to compile mods, I would no longer be able to receive automatic updates (I use Steam Workshop), and with a lot of mods being so new and still in progress, that just won't work. I have come up with a solution to this in my mind, that could probably be easily done by Bethesda, to try to eliminate the confusion and clutter that the current interface offers. As of right now, you can't even sort by Mod name, or whether they are subscribed or not. I think that Bethesda should add a feature to the CK that would allow Mod Creators to add a "tag" to their mods (from a preset list, stuff like "Weapons" "Armor" "City" "NPC's" "Interface" and so on, and then in the Mod Interface you would have several expandable lists that would contain your mods. There would be a "Unknown" list for those mods that do not have tags on them, and that you could easily take into CK yourself and stick a tag on. This would make it to where you could easily find what it is you are looking for, especially for someone like me that has over 100 mods (over 20 of which modify towns and such) and would immensely help in seeing if you have mods that do similar things (Like how there are multiple mods that modify Riften, and I have a few downloaded because I am trying to decide which one I like the best.) Another thing that would be IMMENSELY helpful is if the .esps and .bsas were the same name as the one that Shows in the Mod Interface. I have several mods downloaded that are named one thing in the Mod Interface, but I have such a hard time finding the .esps for because they are named something different entirely. I have a mod downloaded called "Legible Road Signs High Res" in the Mod Interface, but I believe the name of the .esp is "sign" and that makes it really hard to organize. Does anyone else agree?

Look into BOSS. It has a categorization feature. Also, compiling mods together would be a terrible idea for a number of reasons, mostly as it would be REALLY hard to do if you're not intimately familiar with Version Control.