Why wont you acknowledge the difference between a mono-type team and a mono-species team? Well, not mono-species because that would be retarded, but multiples of the same Pokemon.
A mono-type team is going to have six different Pokemon of the same type. What about secondary types? A mono-psychic could have Bronzong, which introduces a Fire weakness. A Celebi introduces an Ice weakness, and x4 Bug Weakness. Etc. A mono-type team, with species clause, is going to have lots of weaknesses.
A mono-species team only has the weaknesses of that one Pokemon. Since you claim people are only getting upset because Garchomp and Salamence are overpowered, let's go with six Bronzong. If they've all got Levitate, that's a grand total of one weakness: Fire. How many Fire-type moves do people usually run on their teams? Not many. Any non-STAB'd Fire move that doesn't OHKO Bronzong is getting met with a swift Explosion. Now what? Things are looking pretty bad.
Now, I'll openly admit this right now so you don't latch onto it in your next post: Mono-species teams only having one or two universal weaknesses is not the reason they're broken. At all. What is does do, however, is disprove your theory that mono-species teams would be weak for the same reasons a mono-type team would be. They're not.
And I repeat: The only reason people are constantly re-using Garchomp and Salamence in their examples is because they're two very good, very common Pokemon that are perfect examples of why allowing more than one of a single species per team is not ideal. That point doesn't change, it just becomes less of an issue as you move down the list. Six Lucario is something I wouldn't want to face. Six Blissey... I'm not too worried. Six Surskit? I forfeit.
The point is, unless you ban the best, most versatile and most destructive Pokemon in OU, it just isn't feasible to remove species clause. The only other option is to partially remove it (You can use as many Sceptile as you want, but only one Garchomp/Salamence/Lucario etc), which just makes the rule needlessly complicated and frankly obsolete; Nobody is going to use doubles of Pokemon deemed not good enough to be banned from having doubles, are they?