To fully simulate bitcoin, you need to make use of the infinitely lowering reward and transaction payments, together with limited money supply. It will create new dynamics, so that it may be efficient to mine a popular chain while the reward is low, since the chain is used frequently for buying stuff and thus has some income from transaction costs.

You can also imitate lost coins by requiring 0.3% fee on all transactions, but giving the miners only .15%...

Another thing would be to implement device classes, to simulate GPU and CPU chains like bitcoin vs. litecoin, so if someone will buy a lot of vASIC devices for bitcoin, he'll not be able to mine scrypt chains since his hardware just isn't capable; CPU would mine really slow on sha256 chains, but would be realatively quick on scrypt chains and someone could think of scrypt vASIC.

And a lot more. This is probably far to the future, but is worth doing, since the simulation now is just missing something...