Two phase commit has failure modes that paxos and raft address.
Raft/Paxos is to make sure majority of the replica for a partition have the latest version of the data and that you can keep writing even if minority of nodes in that partition are unavailable. while still giving guarantee that no write get lost and all read reflect the most recent write.
While 2PC is to write 2 records atomically when the 2 record are located on 2 different partitions.
edit: Looking at the paper, it looks like the tradeoff is increased amount of coordination needed.
"The Two-Phase Commit protocol is thus the degenerate case of the Paxos Commit algorithm with a single acceptor."
I suppose in Spanner, having more than one acceptor is redudant since each shard is a Paxos group anyways.