It’s a deliberate design choice to force the player to make decisions. Or else we end up like in Titan Quest where you can pretty much max out every skill from the two masteries because there are so many skill points.
Deliberate design choice when the game came out. If they could remove skill points in patches I’m sure they would alter the amount of investment you need to put into skills.
Because they are your partner, your weapon and your armor.
What’s more, skills can be balanced. I think, if it’s better to have more pet mutation branch skills than to occupy skill points, such as choosing between better quality and more quantity. Of course, it’s going to be a big job.