but there will be thousands of starters breed while there is still a comparably small amount of mewtwo/mewtwonite. they're not equally rare. maybe for someone who only has a single friend to trade and no way to get on wifi, they would be equally rare. but thats not the reality.
its not like back in red and blue, where another eevee or the other starters or the other fossil were almost all equally rare and valuable in a trade.
both games version exclusives have a similar value in a trade
both games title legendary have a similar value in a trade (though I wouldn't even be surprised if they weren't version exclusive in the end)
the three kanto and kalos starter pokemon (for kanto starters, its more like their mega stones though) have a similar value in a trade.
but those values are not equal. specially for those you can't freely multiply
people know that, even if they don't have any other way to get another starter (if they even want another starter by the time they make it to mewtwo, if its not a event pokemon after all) they know theres dozens of people who are looking for starters and who own a starter of their own.and they will go and look to trade with those. not with the crazy guy that wants to trade a starter for their one of a kind mega stone mewtwo. (which they could trade for something much much better)