Hey there. So... there is one thing that does seem discerning: the Expert and Rigorous Training Skills. The expert skills cost 3 special skill points and they only raise an individual attack stat by one point depending on the class. The Rigorous Training skill raises everything but Dexterity by one button press (10 points for HP and MP, yet 1 point for everything else), I can't name ANYONE who used the skill due to its high price (16 skill points).
I think the removal of the expert and rigorous training skills would work best, mainly because...
1. There are skills that are more worthwhile than those skills, ex. Dash, Pet/Guild Heal, MP Restoration, etc.
2. People are gonna repeatedly buy and use books like it's Black Friday anyway.
To make up for the removal of the skills, here's a little something. ONE extra skill point per level. Yes, instead of 3 skill points per level, you get 4. Come on, pets can gain up to an equivalent of 17 skill points per level (50 HP, 4 Power, 4 Defense, and 4 Dexterity) depending on pet love, base stats, and random chance. Of course this would mean having to give players an extra skill point for all the levels they went through (I'm at Level 197 as of this writing, so I'd have to be given 196 skill points), but the buff would still make up for the removal of the rather useless skills. Besides, people are still gonna drink book shakes anyhow, which would make said buff STILL ineffectual later on.
So yeah, there's my take.