As per the post i made above about the costs and storages increasing exponentially and in a linear way, I think that there should be an exponential increase in cargo limitaions.
I don't know the equation used for the aforementioned, but that should be a good start.
Maybe increase the % of Cargo Space per Trading Port level and per economy future research level. Palace could be a help for that and or relegion, (either adapt a current one or create a new one for that).
Also you can use the above to increase the cargo ships limit.
I'm sorry i don't use numbers but i don't have the equation used in the aforementioned costs and storages. The ships should increase at a slightly lower rate though to not be exploited.
Regarding the pillaging i think you could use a % efficiency based on level to protect the lower players. For example right now if you have let's say 200 ships you can transfer 100k resources. which is 4% of the max storage. If lets say you pillage someone and you can take 1 million resources they should be capable of having at least 25m in storage. Right now looting 1 million sounds a lot but when you get to 100m storage which is not that far way, you can only pillage 1% of the overall storage limit.
So an idea would be to decrease the maximum cargo space in pillaging by 5% for every level in Palace difference. (Could be something else that i haven't thought of yet.)
Also is to possible to inform us when something has been ruled out about the future upgrades? What i mean is for example: People discussing the increase in building slots for 8.8.2. If you know that it will either increase by one or not at all could we get the info that it will definitely not increase by two or more? That would help us a lot with planning ahead.