Top memorable suggestions for me:
Raids
Mandatory Emissary Flags
I'm sticking to things discussed in the video, though I have many many opinions on what is wrong with PvP.
First Raids:
Raids make sense for this game, especially if they can make use of the portals to create instanced content / dungeons, thereby allowing for tall tale level quality and more controlled, crafted encounters. I think these could feature both cooperative challenges, and competitive / invadable instances.
I've thought about this before, and my belief is that there should be a series of standard dungeons you can run once you hit pirate legend for a large doubloon cost, which offer much more difficult challenges, cosmetic rewards, or gold. However, there should also be dungeons that force crews to come together organically, with each crew contributing an item to initiate the dungeon. Something like combining a ritual skull and athena chest to create a special dungeon with special rewards. In other games, we called these items "ingredients" and multiple people would be needed to contribute because it was rare that any one person had everything needed.
Additionally, some of these ingredients would become something locked to your character and selectable at a later point (like your quests) with the ability for you to use it in the future to initiate end-game dungeons, either within your own crew or with another crew. Every crewmember might have something of value they can contribute and parlay into better and better rewards.
These more advanced dungeons could theoretically become something crews fight over competitively (i.e. multiple crews compete from the start / ante up to compete in), or that other crews could invade to steal your winnings, assuming they gamble enough treasure to justify their entry into your instance that is. The important thing though is that this is content you can actually truly fail, and lose your investment or even the treasure from dungeons you succeeded in previously and decided to risk. THAT is end game content, with experienced pirates using the looking for group posts to find people with specific items they can contribute, specific skill sets, and knowledge about how to best beat the dungeon. Make the game less about grinding for rewards, and actually creating the right composition of teammates to earn them.
Next, Mandatory Emissary Flags:
I've suggested a system previously that would simply ask player when they queue in if they want to fly an emissary or not, but that the choice to fly or not would be permanent once they are loaded in to that server (i.e they can't fully lower a flag without maybe voting to permanently lower it), and can't raise later. I should clarify that the system should allow ships to switch emissaries at will, but that lowering them completely is not possible once you opted in.
My belief is that a lot of new players don't understand the emissary system, or simply don't care to learn it, and by forcing the choice would educate themselves on the benefits and risks, which I think would increase the number of flags flown. Additionally, by forcing the choice and making it more normal to be flying a flag, it removes the "take that" element from lowering your flag before fighting by making flags just a normal thing and not some giant target on your back.
Making the flags mandatory to level the faction after a certain point is an interesting idea brought up in the video that would certainly help, but I think by forcing it only after level 75 to level 100 would be missing the majority of players still.
Everyone should want more players to be flying emissary flags. For PvP players, the reason is obvious, more targets, and so less reason to server migrate at all. But that also means more decoys for non-reaper emissaries who now are no longer the only emissary and thus immediately targeted by server hopping grade Vs.