Cryptonite is the first implementation of the mini-blockchain scheme, a scheme designed for maximum scalability, achieved by addressing the problem of blockchain bloat and providing a solution which allows all old transactions to be forgotten by the network after they become old enough. This allows new nodes to synchronize with the network extremely quickly and allows existing nodes to free up disk space by deleting old transactions. As a result of this scheme the network doesn't need to become increasingly centralized only by nodes capable of handling the full blockchain, so mining can remain more decentralized.
Thanks to the mini-blockchain scheme Cryptonite has superior support for micro-transactions and custom transaction messages attached to transactions. In Bitcoin and other altcoins where the full blockchain is required to synchronize with the network, small value transactions and transaction messages tend to be discouraged because they cause "blockchain bloat". The scalable nature of the mini-blockchain scheme relieves us from the concern of blockchain bloat and we can have full support for transaction messages and micro-transactions because nodes don't need to store transactions forever.
Cryptonite is the first altcoin to feature withdrawal limits, allowing users to set a limit on how many coins they can send from an address in one block. This is useful because it helps to prevent double spending and increases confidence in low-confirmation transactions. If a merchant can see that the withdrawal limit on an address prevents it from being emptied in a small number of blocks they can have much more confidence in any transactions sent to them from that address, even without any confirmations at all. So the main advantage of withdrawal limits is that 0-confirmation transactions become safer in the right conditions.
If the claims of Mt. Gox and other businesses are to be believed, transaction malleability has caused quite a bit of damage to the Bitcoin economy. Of course even if that's the true reason why Mt. Gox went out of business, it's still their fault for not understanding transaction malleability when it was well known about for a long time. Cryptonite features unmalleable transactions in order to avoid any repeat of such undesirable events and allow the transaction ID's to be reliable. This is achieved by having the sender sign the txid and by ensuring the txid will always change when the contents of the transaction changes.