Whitcomb!
Welcome to the game mate. I have a few responses to a few points you made in your comment.
1. The Guild Based Bonuses (depending on the guild) would actually help and further the "physicality" that you speak of. If you are in a guild that focuses on "Battle" based tech, this will aid you. If other guilds choose to focus on "Trader" techs, this will also aid Pirates/Privateers as they will be able to raid those fat cats who will get fatter quicker.
2. Transporting resources to Embassy: First not all members in your guild will have their Hideouts in the same port. So a guild won't be transporting resources all to the same spot, forgive me if I misunderstood you on that point. In addition, with "Player Markets" now, you don't have to have trade ships for resources. Yes you will pay more for not transporting the good yourself, but a Player Based Market System will get a boost from a mechanic like this. I am pretty sure CJ would like this point as would those fat cat traders. But yes, you can transport yourself, so be on the look out for pirates or if you be a pirate yourself, look for good targets!
3. Embassy = Virtual Bank: First, Embassy like Banks will not be able to be plundered or attacked. This will be a place to store goods to level up. But the main thing about this is, once goods are deposited they cannot be taken back out. They are lost forever to the person that donated them. Which means they didn't make any money off it. They will be doing this to benefit the guild as a whole. So some decisions will need to be made on how much profit they want to lose to help the cause!
4. Guild vs. Nation: This is a tough one. Depending on play style it can be a conflict of interest. If you be a pirate or privateer, I would suggest you find Like Minded players, form a new guild/nation together and run it like your stole it. I know a few who have done this and have been successful. It does help to have all nation members in the same guild when under attack. You just need to decide how you want to play the game mate and make it work for you.
5. As far as "Attack-able Buildings", I really hope we get some sort of FORTS soon, so we may attack buildings in ports. Read up on that topic. Its a good one and hope it comes next in development.