I personally do not like class-based systems. I'll make a minor exception for games where you choose you class after completing the beginner portion of the game, especially if having multiple classes is an option and is developed into a faction reputation system. It can add to the story if you have to go make friends with the shapeshifter enclave in order to be able to learn shapeshifting from them, and ditto for the thieves' guild and the ability to rob monsters. But mostly I think it's inappropriate to make players choose which fraction of the game to limit their character to before they even start playing.

I generally like skill-based systems, though I have seen some pretty terrible ones too. I much prefer "flat" skill based systems to "tree" skill based systems. A tree system often requires players to permanently waste points on prerequisite skills they don't want before they are allowed to spend points on the skills they actually are interested in, and some tree systems require the player to choose between mutually exclusive branches. A "flat" system means 1 skill point can be spent by any character in the game to learn level one of any skill in the game. (Except skills which are rewards for specific quests or dungeons; it's very cool if some skills have to be unlocked by gameplay, though preferably it should not require a high level to do, if the game has levels. (Skill-based systems are highly compatible with levelless RPGs.) And doing quests or dungeons to unlock or upgrade a skill seems like a better option than grinding using that skill.

My ideal system would be one where playing long enough would enable me to have my character learn EVERYTHING. And it shouldn't take a month to earn a skill point at high levels either. Also I like a feature where I can "forget" all my skills, getting the skill points back to re-spend them. (Probably sacrificing reputation points to do so.)

Crafting IMO should have a different system from combat skills. Crafting should be advanced by crafting, but not grinding; it's much better to require the player to craft tools and appliances as prerequisites for crafting various types of items. For example, crafting a knife to enable skinning, crafting a firepit to enable basic cooking, crafting a cauldron to enable advanced cooking, crafting a kiln to enable pottery, etc. The player is paying time and materials to advance, but they have more fun and feel like they are getting more for their efforts than leveling up crafting by crafting 10 of the same useless item and failing at half of those attempts. (Yuck.) It might be ok for exploring skills, like swimming, shapeshifting into a faster form for traveling, improved sensing of gatherables, etc. to be paid for from the same skill point pool as combat skills; this could cause an economic problem if skill points are hard linked to player levels though.

A different idea for a skill-based combat system is a tactical combat system where the skills are placed onto units (e.g. pet monsters or hired NPC fighters) rather than onto the player. The number of skills which can be placed onto any one unit can be limited, and that limit could be increased through some kind of gameplay (either leveling up the player's monster-breeding skill, or gaining exp on that individual unit, or capturing a higher-level variant of that unit from the wild, or crafting a "+1 skill slot potion" and using it on the unit, etc.) The skills themselves might be craftable too, perhaps as a scroll or rune or gem of some sort. I think this kind of system might be more interesting than just putting the skills on the player, because you might want to use a skill on more than one unit of your team, and whenever you get a better or prettier base unit you might need to buy or make a whole set of skills for it... it's just a more complex system and thus has a lot of potential to be interesting for players to interact with.