I used TweakMB to change base income levels, but I have noticed that the vast majority of villages I've visited are at max prosperity. Even after getting raided, after the village is 'rebuilt' it seems to be instantly (or possibly very quickly, before I could notice a change) returned to full prosperity.
EDIT: I actually switched back to stock income levels without remembering so that shouldn't matter.
I don't usually pay attention to prosperity at castles/towns because I've never actually owned one (is it just a massive grind to get to that point or by 200 days in should I have more than just 2 villages?). That said, I have noticed that Towns are usually at a high level of prosperity, but I'm not familiar enough with the town wealth flavor text to say for sure. What I do know was that the Vaegir town the Guild Master claimed was the 4th-poorest around still had very positive flavor text.
The biggest economy change I've noticed is that I'm having a hard time making money from trade, much more than I used to. It seems to be that bid/ask spreads blew way out, so even goods in abundance that should be cheap/don't fetch much when sold are relatively pricey to buy. With a moderate Trade skill (3 or 4), and depending on the town I visit, I used to be able to reliably get offers (if not from the first town, than generally from 1 or 2 after) for trade profits in the mid-high 100s, sometimes more. Now it's pretty rare that I see predicted profits over 60 or so, and often when I do, when I start lifting bids I drive the price way up so as to make further buying unprofitable.
So overall I think passive income is much improved, I always felt that villages were a little pathetic, but either I'm doing it wrong or trading isn't worth the time anymore.
Also it's really hard to find Furs now, the coat-making quest (not sure if this is stock or diplomacy) is now damned difficult because that ingredient is so elusive.