I use AFT right now but I heard there are some buggy issues and ai problems, the author is also no longer working on this mod... I heard good things about EFF though... I do use custom followers added to the game such as Inigo, Hoth and Vilja... I may also install interesting NPC's ... I'm not super eager for multiple followers, at most I plan on having 2 followers at a time... more interested in stability, customization and behavior of my followers.

If you are not that eager in using more than 2 followers, I would suggest delaying using multi follower mod. If you really want to install one...I would suggest...Vilja.

Vilja's "keep Vilja company" dialogue option can free up your vanilla follower slot...and in some weird way, Vilja IS a multi-follower enabling mod. Works great with "dumb" followers.

And if you like Serana...there is a vanilla bug that will allowing having Serana while still be able to recruit a follower using the vanilla follower dialogue quest.

To answer your question...I have good experience with EFF (non-beta) in terms of mod compatibility. AFT has great features, but the way the author coded it (e.g., its own follower dialogue quest has a priority of 70+, which can block many unique follower dialogues / quests / animations) is known to cause quite a bit incompatibility (e.g., many Cerwiden's dialogue will not fire, and same goes to follower animation from "Dine with Follower").

Vamyan, author of "Follower Compatibility" and is working to update UFO. You may want to take a look at those.

Hope it helps.

If you intend to continue your play I'd switch to EFF once is out of beta. If you really want to start a new game asap you should probably start directly with the beta and not let the new saves see AFT too. I'm not a huge fan of the new interface as it is now but hope it will improve out of beta, I'd still use EFF even if I'll decide to go with the dialogue mode.

I've tried both (twice for AFT, many times for EFF), and both are good, but I prefer EFF. Previous discussions on the forum have shown a preference for AFT, but not by a lot.

I think it mostly comes down to the new follower wheel in EFF. It bothers some people, but I like it. I don't think the look fits Skyrim, but it's very convenient and speeds up interactions, allowing you to bypass all the dialog and quickly get things done. Or to put it another way, to me the immersion gained by quickly doing tasks and getting out of the UI outweighs the loss of a UI wheel that doesn't entirely fit the game.

There is also UFO - Ultimate Followers mod. While I have not yet tried neither AFT nor EFF, I can say nothing bad about UFO. It worked/works for me and I just kept it. Just saying. If I needed to, I would also look into EFF.

^ I read on UFO's forum posts, it's been getting some bugs/issues with the latest Skyrim patches due to not having been updated in a while. Unsure if they're fully gamebreaking though.

I've never used AFT before, but I like EFF because of the ability for in-combat orders via its menu system; and also because it was pretty compatible with Interesting NPCs. Though a lot of things might have changed and AFT might have duplicated some of EFF's features as well. I'd also say to wait for EFF to go into a new full release as the next update is soon™.