It also tends to assume that no one could work out how to fight against six pokemon with different movesets that you can't predict, despite how every time I battle I must go against 6 things with movesets I do not know. Sure, blissey is on every team but does this one have sing? Toxic? Protect and wish? Anyways.
I'm sorry, but that's completely wrong and ignoring several important factors.
Firstly, yes: You don't know each exact set your opponent is running until you've seen their moves. That has no bearing on this discussion whatsoever. The obvious difference is that having multiples of the same Pokemon adds an entirely extra layer of guessing. Sure, I might see Salamence and think "Fuck, what's its moveset", but that's a guess I have to make once. After they've made their first move I know whether I'm dealing with a DD, Specs, Band or mixed variation simply by looking at what attack they used and how much damage it did.
At this point I have no way of knowing if they're carrying another Salamence. The point is, in a regular battle, you'll have to guess the set of every Pokemon you see
once before you have a general idea. In a metagame without species clause, you'd have to guess the set of your opponent
every single time he switches in a Pokemon, because you simply don't know if the Pokemon you're looking at now is the same as the one you were looking at before. Until you've seen six different Pokemon, your opponent could be carrying a double of any of the Pokemon you've seen so far, so you have to guess every time something comes in. That isn't strategy. That's a coin flip.
Your "workaround" isn't a good solution. Because that, again, adds another element to the game that is separate from the battle itself. Instead of thinking "The opponent's Blissey has Twave/SToss/SB/IB", I'll have to think "The opponent's Blissey named Fat Whore has Twave/SToss/SB/IB". And I'll have to remember the nickname/set combination of every Pokemon my opponent sends out on the off chance that they have a second Pokemon of the same species hanging around. Why should we alter the game so that our ability to memorize nicknames mid-game is just as important as, if not more so, than knowing the general capabilities of common Pokemon beforehand?