In a CRPG (Neverwinter Nights, etc.), is it better to have a class-based system akin to D&D or Pathfinder, or a loose skill-increase system?

I find its better to have class based.
When you're assembling of team of players, its better that they be vaired, and class base dhelps ensure that. Otherwise you end up with a load of very generic characters with shared abilities everyone vies to use.

That depends on what you are going for in the game.

*Most* cRPGs use a class system so that players have a harder time designing a party that isn't capable of overcoming obstacles.

That being said, the extremely popular Divinity: Original Sins series has used a much loser and more flexible system, that encourages players to combo their abilities in powerful ways. That being said some of these combos are simply better than others.