I am pretty sure that everything you are asking about is possible.

There are really two files that you need to be concerned about:
1) "properties.lsx" in your module's "Data/Mods/(Mod Name)/CharacterCreation/" folder, which is where the stuff like starting attribute points and classes that are available are defined.

2) skillset.txt in your module's "Data/Public/(Mod Name)/Stats/generated/" folder, which holds all of the custom skillset names in the game (including the skills selectable at character creation)

Custom skills are definitely possible; it just requires making a few files in the Data/Public/(Mod Name)/Stats/generated/ folder. I have made a few topics on the subject, including a portion of the "Main Campaign Modding" thread stickied at the top of this forum, and the "AoE Healing Rain Case Study" thread somewhere on this forum (as well as a few other mods by myself).