So obviously best is an opinionated word, but I would like some input on your guys favorite RPG style plugin similar to Heroes or SkillAPI, right now I am currently testing out SkillAPI but I dislike the skill editor part of it and would rather be able to code my own. Heroes was nice but lacked some customization although they are adding a premium version which might be wonderful, I have also tested others but I am not sure which one I should stick with. Thanks!
Try out RPGme, and Magic. They work great. Rpgme: https://www.spigotmc.org/resources/rpgme.7857/ magic: http://dev.bukkit.org/bukkit-plugins/magic/
Does RPGme support custom skill creation? I haven't seen anything about it though i have been looking.
No, if you're looking for that, try Kingdoms+. It's paid, but you can check it out. Magic actually uses its own texture that doesnt modify any normal item texture, and has custom icons for spells. I think you'd like it.