The way I see it, S2 was pretty lazy. They took a system that was fairly polished already and tinkered with it without understanding how it would impact the whole, like how they made a level-up system that heavily incentivizes a degree of micromanagement the UI isn't built to support.

Or take the pig farm: Clear pros and cons in S1; in S2 it's just a bad bakery. Or the perpetually broken ship navigation, and no way to do naval invasions.