The controls are the easy part, sorting through all the junk characters and stages...
Some people set Mugen up in a way to "have it all" so to speak but when you see what is included in "all", you won't want it... Trust Me!
Check out my dir character structure.
Capcom - Darkstalkers - Anakaris
Capcom - Darkstalkers - Demitri
Capcom - Darkstalkers - Donovan
Capcom - Darkstalkers - Jon Talbain
Capcom - Darkstalkers - Lei-Lei
Capcom - Darkstalkers - Morrigan
Capcom - Darkstalkers - Q-Bee
Capcom - Darkstalkers - Rikuo
Capcom - Darkstalkers - Sasquatch
Capcom - Darkstalkers - VICTOR
Capcom - Darlstalkers - BABY BONNIE HOOD
Capcom - JoJo - SHADOW DIO
Capcom - Marvel Super Heros - Dr Doom
Capcom - Marvel Super Heros - Psylocke
Capcom - Marvel Super Heros - Shuma-Gorath
Capcom - Marvel vs Capcom - Akuma
Capcom - Marvel vs Capcom - Captain Commando
Capcom - Marvel vs Capcom - Cyclops
Capcom - Marvel vs Capcom - Gambit
Capcom - Marvel vs Capcom - Hulk
Capcom - Marvel vs Capcom - Iceman
Capcom - Marvel vs Capcom - Jin Saotome
Capcom - Marvel vs Capcom - Lilith
Capcom - Marvel vs Capcom - Spiderman
Capcom - Marvel vs Capcom - Strider
Capcom - Marvel vs Capcom - War Machine
Capcom - Marvel vs Capcom 2 - Amingo
Capcom - Marvel vs Capcom 2 - Black Heart
Capcom - Marvel vs Capcom 2 - Cable
Capcom - Marvel vs Capcom 2 - Colossus
Capcom - Marvel vs Capcom 2 - Dan
Capcom - Marvel vs Capcom 2 - Felicia
Capcom - Marvel vs Capcom 2 - Guile
Capcom - Marvel vs Capcom 2 - Hayato Kanzaki
Capcom - Marvel vs Capcom 2 - Ibuki
Capcom - Marvel vs Capcom 2 - Iron Man
Capcom - Marvel vs Capcom 2 - Jill
Capcom - Marvel vs Capcom 2 - Ken
Capcom - Marvel vs Capcom 2 - Magneto
Capcom - Marvel vs Capcom 2 - Megaman
Capcom - Marvel vs Capcom 2 - Omega Red
Capcom - Marvel vs Capcom 2 - Roll
Capcom - Marvel vs Capcom 2 - Ruby Heart
Capcom - Marvel vs Capcom 2 - Ryu
Capcom - Marvel vs Capcom 2 - Spiral
Capcom - Marvel vs Capcom 2 - T.Hawk
Capcom - Marvel vs Capcom 2 - Thanos
Capcom - Marvel vs Capcom EOH - Captain Marvel
Capcom - Marvel vs Capcom EOH - Arthur
Capcom - Marvel vs Capcom EOH - Beast
Capcom - Marvel vs Capcom EOH - Firebrand
Capcom - Marvel vs Capcom EOH - Hulk2099
Capcom - Marvel vs Capcom EOH - Juggernaut
Capcom - Marvel vs Capcom EOH - Kenji
Capcom - Marvel vs Capcom EOH - M.Bison
Capcom - Marvel vs Capcom EOH - Sabretooth
Capcom - Marvel vs Capcom EOH - ServBot
Capcom - Marvel vs Capcom EOH - Venom
Capcom - Marvel vs Capcom EOH - Wolverine
Capcom - SF - Honda
Capcom - SF3 - Alex
Capcom - SF3 - Chunli
Capcom - SF3 - Dudley
Capcom - SF3 - Elena
Capcom - SF3 - Gill
Capcom - SF3 - Gouki
Capcom - SF3 - Hauzer
Capcom - SF3 - Hugo
Capcom - SF3 - Hydron
Capcom - SF3 - Ibuki
Capcom - SF3 - Ken
Capcom - SF3 - Kenji
Capcom - SF3 - Makoto
Capcom - SF3 - Necro
Capcom - SF3 - Oro
Capcom - SF3 - Q
Capcom - SF3 - Remy
Capcom - SF3 - Ryu
Capcom - SF3 - Sean
Capcom - SF3 - Twelve
Capcom - SF3 - Urien
Capcom - SF3 - Yang
Capcom - SF3 - Yun Lee
Capcom - SF3 - YURI C-TYPE
Capcom - SFA - Charlie
Capcom - SFA3 - Blanka
Capcom - SFA3 - Dee Jay
Capcom - SFA3 - Guy
Capcom - SFEX - Guile
Capcom - SFMisc - Chunli (Athletic)
Capcom - SFMisc - Chunli (Dark)
Capcom - SFMisc - Dan (Cyber)
Capcom - SFMisc - Dan (Evil)
Capcom - SFMisc - Dan (Violent)
Capcom - SFMisc - Ken (Evil)
Capcom - SFMisc - Ken (Holy)
Capcom - SFMisc - Ken (X)
Capcom - SFMisc - Ryu (Angel)
Capcom - SFMisc - Ryu (Evil)
Capcom - SFMisc - Ryu (God)
Capcom - SFMisc - Ryu (X)
Capcom - SFMisc - Sakura (Dark)
Capcom - SFMisc - Zangief (Mech)
Capcom - SFMsic - Ken (Violent)
Capcom - SFSO - Blaze Agent
Capcom - SFSO - Dark Bolt
Capcom - SFSO - M.Bison
Capcom - SFSO - Perfect Weapon
Capcom - SFSO - Sean Matsuda
Capcom - SFSO - Sonic Machine
Capcom - SFZ3 - Ajuli
Capcom - SFZ3 - Sakura
Capcom - X-Men vs Street Fighter - Rogue
Capcom vs SNK - Athena
Capcom vs SNK - Benimaru
Capcom vs SNK - Cammy
Capcom vs SNK - Chun Li
Capcom vs SNK - Dan
Capcom vs SNK - G Rugal
Capcom vs SNK - Geese
Capcom vs SNK - Gouki
Capcom vs SNK - Gouki (Alternative)
Capcom vs SNK - Guile
Capcom vs SNK - Haohmaru
Capcom vs SNK - Hayato
Capcom vs SNK - Hibiki Takane
Capcom vs SNK - Ingrid
Capcom vs SNK - Jill
Capcom vs SNK - Juni
Capcom vs SNK - Karin
Capcom vs SNK - Ken
Capcom vs SNK - Kuroko
Capcom vs SNK - Kyo
Capcom vs SNK - Lilith
Capcom vs SNK - M. Bison
Capcom vs SNK - Mr. Saikyo
Capcom vs SNK - Orochi Iori
Capcom vs SNK - Rock
Capcom vs SNK - Rugal
Capcom vs SNK - Ryo
Capcom vs SNK - Ryu
Capcom vs SNK - Sakura
Capcom vs SNK - Terry
Capcom vs SNK - Todo
Capcom vs SNK - Vice
Capcom vs SNK - Yamazaki
Capcom vs SNK - Yun
Capcom vs SNK - Yuri
Capcom vs SNK 2 - Blanka
Capcom vs SNK 2 - Chang
Capcom vs SNK 2 - Honda
Capcom vs SNK 2 - Joe
Capcom vs SNK 2 - Kim
Capcom vs SNK 2 - Kyo
Capcom vs SNK 2 - Rolento
Capcom vs SNK 2 - Sagat (Boss)
Capcom vs SNK 2 - Urien
Capcom vs SNK 2 - Vega
Capcom vs SNK 2 - Zangief
Film - Misc - Ash
Film - Misc - Omega Tom Hanks
Food - Misc - Colonel
Food - Misc - Donald
Guilty Gear - A.B.A
Guilty Gear - Anji Mito
Guilty Gear - Axel
Guilty Gear - Baiken
Guilty Gear - Bridget
Guilty Gear - Chipp
Guilty Gear - Eddie
Guilty Gear - Faust
Guilty Gear - I-NO
Guilty Gear - Jam
Guilty Gear - Johnny
Guilty Gear - Justice
Guilty Gear - Kliff Undersn
Guilty Gear - Ky
Guilty Gear - LEOPALDON
Guilty Gear - May
Guilty Gear - Millia Rage
Guilty Gear - ORDER SOL
Guilty Gear - Potemkin
Guilty Gear - ROBO KYII
Guilty Gear - Robo Rock
Guilty Gear - Slayer
Guilty Gear - Sol Badguy
Guilty Gear - Testament
Guilty Gear - Venom
Guilty Gear - Zako-C
Guilty Gear - Zappa
Misc - Blockhead
SNK - SS - Zankuro
SNK - AODK - Kisarah Westfield
SNK - Fatal Fury - Tung Fu Rue
SNK - Kim Kaphwan
SNK - KOF - Angel
SNK - KOF - Ash
SNK - KOF - Blue Mary
SNK - KOF - Iori Yagami
SNK - KOF - Leopold Goenitz
SNK - KOF - Mai
SNK - KOF - Mature
SNK - KOF - O-Adel
SNK - KOF - Ralf Jones
SNK - KOF - Ryo Sakazaki
SNK - KOF - Shingo Yabuki
SNK - KOF - Terry Bogard
SNK - KOF - Tizoc
SNK - KOF2K - Vanessa
SNK - KOF2K3 - Mukai
SNK - KOF2K3 - Terry Bogard
SNK - KOF97 - Orochi
SNK - KOF98 - Rugal Bernstein
SNK - KOFMisc - E-Terry 71113
SNK - LB - Akari
SNK - LB - Minakata Moriya
SNK - LB - Zantetsu
SNK - Misc - Kaori Yanase
SNK - SS - Enja
SNK - SS - Gaira
SNK - SS - GEN-AN SHIRANUI
SNK - SS - Genjuro Kibagami
SNK - SS - Haohmaru
SNK - SS - Iroha
SNK - SS - Jubei
SNK - SS - Rashoujin Mizuki
SNK - SS - Senryo Kyoshiro
SNK - SS - Shin Galford
SNK - SS - Sokaku.m
SNK - SS - Suijya
SNK - SS2 - Cham Cham
SNK - SS2 - NEIHALT SIEGER
SNK - SS3 - Hisame Shizumaru
SNK - SS4 - Amakusa
SNK - SS4 - KAZUKI KAZAMA
SNK - SS4 - Nakoruru
SNK - SS4 - SOGETSU KAZAMA
SNK - SS4 - Tam Tam
SNK - SS5 - Enja
SNK - SS5 - Karakuri Ocha-Maro
SNK - SS5 - Kusaregedo
SNK - SS5 - Mina Majikina
SNK - SS5 - Poppy
SNK - SS5 - Rera
SNK - SS5 - Rimururu
SNK - SS5 - Sankuro Yorozu
SNK - SS5 - Yoshitora Tokugawa
SNK - SS5 - Yumeji Kurokouchi
Super Hero - DC - Batman
Super Hero - DC - Deadpool
Super Hero - DC - Flash
Super Hero - DC - Lobo
Super Hero - DC - Wonder Woman
Super Hero - Marvel - Captain America
Super Hero - Marvel - GhostRider
Super Hero - Marvel - Sandman
Super Hero - Marvel - Thor
TV - Family Guy - Chicken
TV - Family Guy - Peter
TV - Film - Mr Increible
TV - Film - Rambo
TV - Futurama - Leela
TV - Misc - Fat Albert
TV - Misc - Fred Flinstone
TV - Misc - Liono
TV - Misc - Popeye
TV - Simpsons - Bartman
TV - Simpsons - Burns (Vampire)
TV - Simpsons - Evil Homer
TV - Simpsons - Homer
TV - Simpsons - Homero
TV - Simpsons - Krusty
Video Games - Misc - Orchid
Video Games - Misc - Pacman
Video Games - Misc - Rac.people
Video Games - Nintendo - DuckHunt
Video Games - Nintendo - Master Hand
Video Games - Nintendo - Sandbag
Video Games - Nintendo - Super Mario
Video Games - Sega - Sonic
Do you know how much time it took me to sort all of it neat like that!?
...and that is not even my final version, it's just what I have here last at work!