Ooh ooh, I got dis. If you only want one hero and have its skill points show up, then I think I have the answer.
1) Create a dummy hero ability. The amount of level it has depends on what you want to do.
a) Do you want to follow the normal wc3 style, earning a point per level up? Set the spell levels to the maximum amount that you want (if max hero level is 50, then set the skill level to 50)
b) Otherwise, if you completely customize it, then just set the skill level to 1. Speeds up loading time that way.
2) Give the ability to all heroes that use this.
3) Use a trigger to DISABLE that dummy spell for all players.
4) Enjoy if this is exactly what you want. Heroes will still earn skill points for all hero spells that they have, even if it is disabled. I remember this from one Blood Elf Campaign where you play as Kael, and you hit like level 8. But your Phoenix is still disabled. Regardless, you still have a skill point.