i think the best solution would be to code something in the core that rejects a block if it has no transactions.
this way the pools that mine empty blocks get NO REWARDS.
Not a bad idea in itself, but they could just create 1 satoshi transactions to put in those blocks. Hence they wouldn't be empty anymore ^^
What's could maybe help, would be to only allow to mine full blocks no?
If only full (or let's say 80% full) blocks were minable, it would make transactions a bit slower but would also answer the size problem for now no?