did you play with RNW? I've tried a couple mods which are supposed to improve it but i still find i am largely disappointed by its results and have gone back to playing without it.
I wanted to but forgot to ask the host about it ;_; I'm especially interested about the "fantasy new world" option where you can basically have a chance to spawn civilised/technologically advanced nations in the new world
I've never had the chance to play a MP with it as of now.
I think the estates definitely need some working, the base autonomy loss from the distribution of provinces remains a huge problem for me and makes me unwilling to give any more than the required provinces, it also seems incredibly hard to keep the influence and loyalty of the merchant classes and they seem relatively weak compared to the other estates (i mean who the fuck ever really needs diplo power after all?).
The estates are somewhat different country per country. Maybe the country you had with those issues is "bound by the game" to have problem with such or such groups. For the countries have been playing as, I've felt that, indeed, you want to have estates have as few provinces as possible under their control, but even that minimum threshold is quite high and force you to have a large chunk of your territories with -25% autonomy. The bonuses, for me, balance it all if you manage both loyalty/influence. I've found that when you have enough money and prestige (or other "currency" to buy loyalty) its totally worth it to increase loyalty and sometimes influence to reap the most rewards, through the estates interaction panel.
Things like +20% trade efficiency, as Voncrow said, is completely OP. I'm the 1st trade income nation, in part thanks to that, I believe.
Nobility giving you -10% land maintenance, +20% manpower modifier, is extremely useful too. And the clergy with -% development cost and overall stability
I know there is other kind of estates but I didnt play enough countries to know them.