i would suggest a few behaviours that could slightly alleviate some of the complaint:
1) whenever you see a book seller mark it on the map writing what type of book it sell, so you at least have not to run between many location trying to remember where it was the one you search
2) when you see a book of a skill you definitely would use buy it immediately then put it in a bag, when you levelup and free some more skill slot open the bag and see what you have at disposal without need of going back to town.
3) put one of the pyramid near the seller you use the most so that you could instantly teleport to him wherever you are
I understand the complain about the skillbooks, they are not a perfect solution for everything but they are not so bad.
i will try to respond to some complaints:
unrealistic: you should simply think of the skillbooks as of magic books that when read bestow some skill that the writer impressed in it and then the magic charge disappear and became a useless (or blank) book, it's a think that existed in D&D 30+ year ago but it was much more rare, in divinity everyone with craft high could do it, so it's reasonable that there are more books available and seller specialized in it.
the characters are busy people, they need shortcuts in the learning process that usually take many many years
for a warrior maybe it's realistic to learn new trick fighting, but for the same warrior it would be rather unrealistic to level up, put one skill point in water magic, and out of the blue learn to cast three spells.
limit to freedom: the randomness of what is available could be upsetting for someone used for example to diablo3 where you could continually respeck and try new combination, or simply had a specific idea of what is character must evolve into, especially for someone that want to make a pure melee fighter or pure thief assassin;
for other people (myself included) it could instead be a stimulus to try some skill that you would instead skip and find new synergies from the group abilities, it's rather a boon to people that would instead stick to a specific build and never experiment the variety of the game
break of immersion: levelling up and feeling forced to interrupt the current quest and go back to town to acquire skillbooks is a totally subjective complaint, even stopping the advancement in the quest to think what skill you will improve is a break of immersion in the story.
you could simply wait that you end the quest for a resting period in the town where you relax a bit and improve yourselves, even in the pen and paper d&d you doesn't make the levelup during a fight or a playing session, you wait for a break in the story.
also with all the teleport options (the pyramids expecially) you could avoid all the walking and be back to questing in no time.
