Right now, we are seeing version 1.0 and version 1.1 of cryptocurrencies.
I can see a version 2.0 of a cryptocurrency coming out, with some features to help:
1: Escrow. It would be nice if a third party, Charlie, could be part of the transaction, and Alice and Bob's transaction it wouldn't be completed until Charlie gives the OK. If Charlie doesn't give the OK, Bob doesn't get the currency... eventually after a selected timeout, the coins wind up back with Alice. Or, it could be configured the other way, where Bob gets his coins if Charlie doesn't step in and say "no" after a period of time. Of course, there can be collusion between Charlie and either Alice or Bob to fuck over the other party, but having the -option- for an escrow service so both parties are happy would go far in making a currency usable for trades.
2: Auditing. The ability for a party to tag their own expenses with their own ID for something, so they can in the future run through the blockchain, and find all occurances of that ID. It would be equal to the "For:" line on a checkbook.
3: Refunds. The ability for both parties to reverse a transaction, on the premise of the item in question being returned. This will go a long way in proving ownership of something if it gets questioned.
4: Disabling spending of currency for a period of time. This adds a "timelock" value, so if the currency owner is going to be gone for six months, even if someone has access to the wallet, the coins can't be spent. Of course, once the time expires, it becomes a race between the legit owner and anyone else who has access to the wallet's private key, but it is a way to ensure coins are not going to be gone while someone is on a trip. Of course, this value should be limited to a fairly period of time (6-12 months), so coins are not tossed out of the economy permanently.
5: Similar to #4, but disabling spending of coins for a period of time... but allow them to be re-enabled if another wallet or private key gives the go-ahead. This way, one can have one wallet that coins go in, set a time lock, but still have an offline wallet that can re-enable use of the coins should the need arise.
6: A way to mark part of the transaction as sales tax (with the receiver agreeing on that), so the sender is showing that the 110 units they are paying, 100 are for the product, the rest are going for taxes like a VAT or the like. Similar to #2, but covering the tax angle. In case of audit, it would be easy to just show the blockchain and that the receiver acknowledged that the tax was properly paid.
7: A way to preen the blockchain after a period of time, say seven years of older transactions, but still keep the crystallographic integrity of the entire thing. This way, eventually, the blockchain size will tend to stabilize as soon as old transactions get expired.
I'm sure there are other ways, but adding some cryptographic tricks (like escrow and moving coins out of play for a period of time) will definitely add to currency security.