Cooldown vs Mana
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At some point during development you need to find a way to limit player's access
to special abilities, and the two most common ways to do that are cooldown and
mana pool systems.

In Caves Of, each weapon gives the player access to one skill only. However,
since the player can in any moment switch to the secondary weapon (or even equip
others from the inventory), he has access to four skills he can unleash on the
enemies.

Given this, which system should I go for, cooldown or mana pool?

I think the main reason behind going for the cooldown is promoting skill
rotation: you can't just spam your strongest skill, but you need to think in
which order you want to activate them. A consequence of this is that skill
synergies are basically mandatory to fully take advantage of the cooldowns
system. However, skill rotation wouldn't be that great in Caves Of. First of
all, while I like the idea of the player switching to the secondary weapon to
activate the skill and switch then back to the primary, I don't want to promote
a pattern of forcing the user to open the inventory screen and equip an axe only
because his equipped weapon skills are in cooldown. Additionally, a mana pool is
also a much easier system to implement, so it's a better to start with it.