CK2+ is basically adding stuff into Vanilla so that it feels basically like Vanilla, but with more everything (it has Chalcedonian Christianity for example, in the earlier start-dates. It gives each main-branch of Christianity a way to mend the schism, or a way to prevent the schism if you start earlier. It has mechanics to make empires collapse, and interesting stuff like Coronation and stuff.)
After the End is a
really awesome total-conversion mod. I cannot recommend it more highly in terms of quality. Especially if you personally live North or Central America, it's just loaded with stuff. Even the
music is A+. That said, the main branch is on hiatus and was never updated for M&M or Jade Dragon, so the Fan Fork is probably a good idea.
HIP is good if you want a more historical playthrough, or much more radically different CK2 gameplay (CK2+ is much more restrained in that respect). It has a huge amount of settings and stuff for determining exactly HOW historical you want to make things. (Also, one thing I found rather neat in HIP was the ability to mark one or more AIs with a "Lucky" trait, which is inherited by their heir and makes them super strong and intelligent ambitious and likely to be powerful later on.)
There's also other mods, like When the World stopped making sense (Dark ages), the Game of Thrones one that I hear so much about, and that Warhammer one "Geheimnisnacht" (which, last I heard, was really good, but fairly slow, although that was a while ago. Wiki says it's still active though, and that was before Reaper's Due made the game a lot faster, so YMMV.) and other mods, but I don't know much about those beyond that they exist and I see screenshots of them occasionally.
TL;DR: Here's a link to the CK2 wiki pages for
CK2+,
HIP, and
After the End. I don't know of any QoL improvement mods that I would personally recommend.