Other than that, there have not been many compelling arguments, of the few arguments that have been made at all, put forth for the repeal of species clause.
Gradient Facade's comments about how having two of the same Pokemon is similar to changing one Pokemon's moveset or EVs are very well-reasoned, but I feel like that sort of revision between battles requires quick thinking and ingenuity, plus it is only effective if the same people continue to play on the ladder. In that case, you're playing off opponent expectations by skillfully modifying your set.
If I bring Taunt Babiri Berry Whimsicott and my opponent is running godsquad and chooses to send his Mega Mawile, then I switch to Moonblast + Occa Berry before the next battle to anticipate his Gyarados or Charizard, that feels to me like a more "deserved" source of ladder points than if I simply bring two Kyurem-Bs** and claim a second consecutive win because my opponent doesn't know if he should stay regular and DD with his standard Charizard X like he did last time (when he lost to my Icium Z one) predicting a Scarf set or mega-evolve and Outrage expecting the Icium Z one again.
In the first situation, there is no
expectation of my deceit; I made a clever move to take advantage of my predilections of my opponent. In the second situation, my opponent might as well flip a coin to determine whether he Dragon Dances or Outrages. Yes, I know this situation could be reversed. I could switch my Kyurem-B from Icium Z to Choice Scarf between battles to screw up my opponent and play mindgames. That requires actual proactivity on my part. My opponent is not thrust into a situation where he automatically faces a 50/50 from the first ladder match's team preview. (Those come later, after the second battle, when we get to the psyching-each-other-out phase and all bets are off.) And I won't even get into how stupid species clause's absence would be in tournament games.
First I don't believe making an assumption as to how proactive people are or aren't is valid reasoning for anything. I'd like to point out that most top players, such as Kentari, Raimon, UnleashOurPassion, etc don't consistently use just one team at a time while laddering, they're always switching teams up, and if things get intense enough, even switching sets on individual mons to achieve the same effect you outlined with the Whimsicott example. Simply put, changing teams is almost a requirement to getting good performance rates in 1v1. Removing species clause would encourage people not only just to learn opponent's sets as they battle, but to beat the mons using those sets completely, rather than falling into the well-hated realm of counter teaming, or just niche teambuilding in general.
Second People aren't just going to use the same set two or three times in the same team when it comes to teambuilding (This may be an assumption, but even if people go against it, it will only hinder the people using them, rather than their opponents). Every individual set has its own grouping of things it beats and loses to, many sets having such a different range of coverage in comparison to other sets of the same mon, that they essentially become a different pokemon by that comparison.
An example of this would be Porygon-Z. The typical Choice Scarf set is used for outspeeding and OHKO-ing many frail threats, while the lesser used Choice Specs set is used for punching right through bulkier mons that normally beat the Scarf set. This effectively makes Specs Porygon-Z an entirely different threat from Scarf Porygon-Z, with Specs being more comparable to something like Charizard-Y.
Since you can already use Charizard-Y along with Scarf Porygon-Z to cover a similar range of threats as Specs Porygon-Z
and more, Why not simply allow us to use the Specs Porygon-Z alongside it instead? Don't you think it's a little suspicious that very few people who took advantage of no species clause, if any, won battles consistently? Not to mention, the lacking presence of good players in Gen 6 1v1 replays who took advantage of no species clause at all, regardless of win or loss, for any purpose other than memes? Exactly. This is because having the same species of mon on a single team acts only as a hindrance to your overall potential viability.
Third The only possible reason I can think of to keep species clause in place, otherwise, is that 1v1 without it would become more "uncompetitive", akin to Accuracy dropping, Sleep, Jirachi, and more. The problem with this idea is that it is mathematically unable to be proven. All the concepts I listed above are uncompetitive, and they all have percent-based chances associated with them, while 1v1 with or without species clause will always be the case of you asking yourself whether you beat the mons your opponent has or not, which does involve risk management, but not typically any kind of fixed chance or gamble that is associated with "uncompetitive" things, similar to picking your lead mon in a 6v6 environment.
Ultimately, I can't provide any reason besides my own opinions that 1v1 without species clause would be better than it is now, just like how I can't change your feelings of whether 1v1 should be 3v3 or the original 1v1. I just implore that you think about it and make the decision that would best benefit the metagame and our community.