It could be because they didn't want you to be able to have multiple of your starters.
You can still have multiple breeding with a ditto but Ditto's are rare and/or only found way later in the game.
You can just restarts until you get a female but that takes time, so if you are really devoted to it you can still get it.
Dittos weren't as rare in older games because they weren't expecting breeding to be this big. Now they are more rare and it is harder to get them.
That's the best thing I could dig up on the subject, I hope it helps. :]
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