I think the point of the version numbers is to define which consensus rules a block follows. Older blocks may no longer be considered valid blocks under new rules, but with the version numbers, clients can identify which rules those blocks follow. E.g. version 2 blocks did not necessarily include transactions that followed the BIP66 rules but version 3 does. If the version numbers did not exist, then we would have an issue where some v2 blocks are no longer valid under v3 rules and the clients would get all screwed up because they have historic blocks that don't validate.

Version numbers also help to facilitate miner voting. Miners voted for using BIP66 rules by producing v3 blocks. BitcoinXT nodes vote for BitcoinXT by producing blocks with 0x20000007 set as the version.