It's a balancing tactic. When a Pokémon uses transform, they copy literally everything about its target except the HP stat. For Ditto, Smeargle and Mew, if they copy a Pokémon with a lower HP stat (particularly notable for Mew, who has a slightly above-average HP stat), they'd end up as just a better version of the Pokémon in play. Of course, you also run the risk of copying a Pokémon with a higher HP than you, in which case you end up with a worse version of the opponent. Considering that it's a Gen I move, it could very well be something that they predicted could become overpowered, as they were inexperienced with how the game would balance out at the time, so they put a little handicap on it and just never saw a need to remove it.
