More specifically, I'm not a huge fan of the fact that you can use multiple worlds to bypass portal restrictions. I actually kindof like what the portal restrictions do to the gameplay, and the fact that loot worlds basically nullify that really bothers me.
Here's the thing. I don't mind transporting resources from world to world in the general sense. I actually really like this. I think it solves one of the major problems that Minecraft has, where you end up starting over from scratch every time there's a new worldgen update. It also makes non-renewable resources effectively renewable by way of infinite worlds. You might think that there's plenty, but if you are playing with some buddies and you all like building really big things, iron starts to get a little tight if you're only looking at one map's worth. Especially when you can clean out 10 crypts in a day (we got about 800 iron this last run) – and then end up using it all almost immediately.
The problem is that, when using a loot world, you basically skip half the gameplay. You don't care about having a permanent base, because you're not shipping anything anywhere. Whenever you need to empty your inventory, you just switch worlds and dump into a chest you have set up for the purpose. I don't think I have to explain this very much. It's been discussed to death in other portal cheese threads.
So how do we preserve the ability to take arbitrary items from one world to another, while also making it so that loot worlds don't simply make the portal restrictions irrelevant? Two things.
If you log out of a world with a non-portalable in your inventory, you will simply drop the item on the ground where you're standing. You cannot take non-portalables between worlds simply by putting them in your inventory.
Put special chests at the spawn altar. The contents of these chests are saved per-character, not per-world. That means that the contents of these chests are private to each character, and they are the same across all worlds that the character plays in. Any changes to the contents in one world will carry over to another one. Non-portalable items can go in these chests.
This way, loot worlds are still completely viable, but non-portalable items harvested in these worlds would still have to be shipped to a central location, preserving that element of gameplay.
As a bonus, these chests can be a convenient place for storing gear that a player might not want to carry on them all of the time, but would like to have access to without having to log out and switch worlds (twice).