Should I increase my mempool size to accomodate temporary crisis? I am seeing 68k unconfirmed transactions on blockchain.info. My own bitcoind (v0.13.0) node has 49k transactions in its mempool with memory usage currently at 230mb. Knowing that the memory cap is currently at 300mb, I fear that very soon my node will not be able to keep all unconfirmed transactions. Should I increase this cap as a temporary measure until things get better? if so, how do I do that?
You can increase the mempool size, if you have an interest in seeing transactions that likely won't confirm for a very long time, but you certainly don't have to. The mempool is sorted by feerate, and when the limiter kicks in, it removes the lowest feerate transactions. Since miners sort by feerate, and can include only a limited number of transactions per block, the mempool effectively works as a queue.

By design, you will not always be able to store all unconfirmed transactions. If your goal would be to have all, and crank up your memory pool to accomodate this, someone could just start creating an infinite stream of transactions sending back and forth, until your node goes out of memory. This is the reason why the mempool size is limited in the first place: protection against a denial of service on the network.