This mod aims to be a complete overhaul of the followers behavior in the game. I am still learning the Creation Kit, so some things are still in the works. I plan to have all the followers in the game changed to the settings below by the end of the weekend (actually the goal is tomorrow) and then I will begin work on the 'Goals' section.

CURRENT CHANGES:
1. No Level Cap: Makes all followers level with you, as far as you go (previously most stopped at 50). Known issue, some followers are glitched and do not level with you at all (this has nothing to do with the mod and Bethesda is working on it).
2. Marry Followers: Makes all followers possible candidates for marriage (untested - this seems like a pretty obvious fix in the CK, but I have not ever gotten married in game and don't know how so I will say this is untested until someone tells me otherwise).
3. Less Agressive: Makes followers (humans - not dogs) more passive. This means they will happily fight along side you ONCE COMBAT HAS STARTED. They won't ruin your sneaking by attacking everything that moves.
4. Fixes the stealth meter: Currently it is extremely difficult to sneak with a follower because they can always see you. This removes your follower from the stealth meter (possible issue is sneaking past a potential companion before they are a companion. It would say completely hidden right up until they reported you - Plans to make a script to adjust this based on whether they are currently your active follower).
5. Removable Armor: Makes followers starting equipment possible to remove by the player.
6. Immortal Followers: If they are 'killed,' they will take a knee and remain that way for 30 secs and stand back up with almost no health (if they don't take any more damage). Dogs can take damage but cannot be knocked unconscious (this is because dogs do not have an 'unconscious' animation.

BATCH FILE:
While I figure out how to implement these features into the main file, I created a temporary fix. A batch file that will apply the following tweaks to pets and human companions. It is very easy to run, just read the readme with it. Sorry it can't be installed through NMM, though. Hope this helps to tide people over.
1. It will make sure your companions are the same level as you every time you run it (even if Bethesda can't figure this out right now, we can create a bandaid).
2. It will give all followers perfect sneak.
3. It will give all followers the light step perk so they don't set off traps.

GOALS:
Changes planned for the future.
1. Make followers more tolerant. While trespassing, you cannot talk to followers, they just judge you. I want to change that, so that they will still judge you, but will also accept commands. I figured out how to remove "You shouldn't be here..." from the game, which works fine for followers... But it effects everyone, not just followers... Still working on it.
2. Give the followers multiple responses (goal is 5) to trade requests so that you don't have to hear the same annoying thing over and over.
3. Change dogs' homes to your homes. Meaning, you won't have to re-buy a dog if you dismiss them, they will simply wait at your house, similar to a wait command.
4. Add a "back up" request to dialog, to get followers out of your way without having to Shout at them.
5. Not sure about this one yet, but I was thinking that on a scripted event when your follower receives a 'back up' request (through dialog or just by walking into them) they become temporarily ethereal. Meaning, you can walk through them. There is no visual component to this.
6. The ability to request a follower hides their helmet via dialogue option. The follower will keep the armor from it, in fact they will still be wearing it, it will just be invisible.
7. Multiple followers option. Allow the player to have as many as they want at once.
8. Include the features in the batch file into the main file, removing the need for the console.

INSTALL:
I advise using Nexus Mod Manager to install. If you do, install is just clicking the "Download with Manager" button, then activating it in NMM. If you insist on manual install. Then mimply place the "Companion Followers.esp" file into the Skyrim Data folder. That's wherever you installed the game. Then modify "SkyrimPrefs.dll" in ..\[USER]\My Documents\My Games\Skyrim\ Go to the "[Launcher]" section and add the line "bEnableFileSelection=1" if it doesn't exist, if it does, make sure it equals 1. The in the launcher go to "Data Files" and check "Companion Followers.esp." Then play and have fun.

OPTIONAL FILES:
*Non-Essential Version: Same as above except that followers can die normally. Erandur, Cicero, and Mjoll the Lioness are all still essential because this is required for the game to run normally. This is a stand alone file and does not require the 'main' file to run. Do not run both. Run one or the other.
*Protected Followers Version: Same as above except that followers can be killed by the player. Erandur, Cicero, and Mjoll the Lioness are all still essential because this is required for the game to run normally. This is a stand alone file and does not require the 'main' file to run. Do not run both. Run one or the other. KNOWN ISSUE: 'Unconscious' followers can still be killed by AoE attacks by enemies, the enemy just cannot intentionally target the downed follower.

CURRENTLY UPGRADED FOLLOWERS:
Mage Followers:
Aranea Ienith
Belrand
Brelyna Maryon
Eola
Erandur
Illia
J'zargo
Marcurio
Onmund

Rogue Followers:
Aela the Huntress
Annekke Crag-Jumper
Athis
Cicero
Dark Brotherhood Initiate
Derkeethus
Faendal
Ghorbash the Iron Hand
Jenassa

Warrior Followers:
Adelaisa Vendicci
Ahtar
Argis the Bulwark
Benor
Borghak the Steel Heart
Calder
Cosnach
Erik the Slayer
Farkas
Golldir
Iona
Jordis the Sword-Maiden
Kharjo
Lob
Lydia
Mjoll the Lioness
Njada Stonearm
Ogol
Ria
Roggi Knot-Beard
Stenvar
Sven
Torvar
Uthgerd the Unbroken
Vilkas
Vorstag

Animal Followers:
Stray Dog
Meeko
Barbas
Vigilance

NOTE:
Please let me know if anyone sees any errors, or let me know if you have any requests or opinions. I am here to serve! Oh, and I know there are a lot of options, even more once I finish everything, and everyone has differant tastes. I plan on building a FOMod Installer that will let you pick which options you want, once I figure out how. Until then, there is only one .esp because there are a lot of potential combinations and, unfortunately, they would conflict if every option was it's own .esp.

Along that line. Obviously this will conflict with any .esp that changes the followers, besides cosmetic ones. Reskins, cute hairstyles, japanese cloths, or whatever you are in to, cosmetically, won't conflict.

Update v1.1
*Added 'Roggi Knot-Beard' to the list of NPCs.
*Made All Listed Dogs Protected and Passive, not effect Stealth Meter, and removed level cap.
*Fixed Lydia to be Protected, instead of Essential.

Update v1.2
*Added a batch file that will make sure your companions are the same level as you, give them perfect sneak, and give them the light step perk (not set off traps).
*Added 'Roggi Knot-Beard' (for real this time).
*Uploaded a non-essential version of the file.

Update v1.3
*Changed the main file to set all companions as essential (cannot be killed, at all) instead of protected.
*Uploaded a protected followers (can only be killed by you or aoe after 'knocked out') version of the file under optional files.
*Sets all dogs to 'invulnerable,' meaning they can take damage but not die (this is because dogs do not have an 'unconscious' animation.

Update v1.4
*Fixed naked followers bug.

Update v1.41
*Fixed Annekke Crag-Jumper, who was still experiencing the naked followers bug.