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The largest advantage is it can lead to lite clients which don't need full blocks and instead can request block headers and merkle branch from other nodes.  This isn't implemented yet and I believe one of the developers indicated it may require a seperate protocol.

The use of merkle tree can also allow blockchain pruning by removing older transactions once a newer transaction for a particular address is deep enough in the block chain.  With a single hash for all transactions this wouldn't be possible not without some mechanism to re-sign the pruned block and that would require some sort of alternate proof-of-work to ensure decentralized consensus.

More generally speaking using a merkle tree allows more granularity in transaction validation.  You can validate an entire block, a group of transactions, or just a single transaction.  Using a merkle tree allows options to deal w/ future issues that the network may need to deal with.

If I understood correctly what you mean is that the entire block will be removed from the blockchain. Wouldn't that compromise the whole blockchain since each block includes the hash of the previous block, and therefore if one is removed then its reference in the next block will be not verifiable (as the block was removed).