It makes SENSE to have more. Normally, wouldn't leveling up mean that you'd also get stronger skills? Meaning that, if you got all your skills at lvl 3, they'd generally be "basic" ones? No fancy final attacks or stuff like that? Meaning that, chances are, their base damages and scaling ratios would be sub-par?

Anyways, Deep Ground is still a game. And having new skills to toy with is part of what keeps people playing~