Pirate faction is limited to 100 players now anyway, housing areas are safezones yes, except when the zone is in War or you're the aggressor. The two most complained about things right now are killing greens gives a few too many crime points and trading system not being great (it's not bad, but not great either). Gamigo, the current publisher, already forwarded these complaints to XL, trade system will stay at least for launch but they're looking into possibilities of bringing back the old system back.
Other changes off the top of my head:
- player nations were removed, current players all say this is a good change because everyone was just congregating into a single player nation and then completely stomping over the server, no challenge
- castle sieges are now faction based, a faction hero (player) leads the siege and afterwards the entire faction can reap the rewards of claiming castles
- lots of crafting gear RNG was removed, you don't lose gear anymore on failed upgrades, you can restat gear somewhat easily. In addition something called Hiram gear was introduced, which was a sort of a catch up mechanic. It's a bit weaker than crafted gear but a good alternative, so you don't rely on crafting anymore if you choose to go with this gearing path
- after 55 you gain ancestral levels and can gain some additional stats and sidegrades for your abilities
- plenty of zones and open world bosses added
- some mercenary system added to help balance out the factions
- new races, ships, ship gear, dungeons
So all in all most of the changes were made to balance stuff out and get as many people to experience all the content as possible.