I think you're worrying a tad too much here.
I've always known from the beginning that not all Pokemon are created equal. You just have to catch two Rattata and see that one has a higher attack stat and the other has higher speed or notice on a second playthrough that "wow last time I played, my Cyndaquil knocked out Falkner's Pidgey in two hits, but this time it takes three despite being at the exact same level!" I didn't know exactly how exactly they differed, but I knew there was variation in them.
If you try to create a competitive team ingame while going through the main quest, chances are you're not going to have a fun time. I tried that once in Emerald and NEVER AGAIN. Running through the grass for hours in the first area trying to find 252 rare wild mons that give you EVs in attack while you have to try several times to escape from the really common mon that gives you EVs in defense instead is not fun. And you won't take on your first gym leader for hours because his mons give the wrong kinds of EVs. Just wait until later when you can get to that patch of grass in the fifth city that buries you in attack giving mons and oh hey you can just fly to the eighth city afterwards to get your speed EVs.
If you try to give yourself six mons for competitive play right in the beginning, chances are you're going to get frustrated or the worst thing happens - you mess up your EV training and now, metagame wise, your mon is ruined. Hope you saved recently or didn't save not realizing you accidentally have given your Slowbro speed EVs. Going through the game normally may not be optimal competitively, but trying to train a metagame team while going through the main quest is a waste of your time and more importantly, not fun. And if there's one thing your game should not be, it's not fun.
Seriously, don't try to make a competitive team until postgame where you have access to all the resources the game has to offer. Items, (POWER ITEMS. VITAMINS. RUNNING SHOES AND BIKE FOR EGG HATCHING) optimal EV training spots, a high level team to help out your new, freshly hatched perfect IV mon, high level enemies for easy leveling...as someone who spent a lot of time making catching, breeding, and raising competitive Pokemon for cartridge play (and I totally intend to get back into it sometime), with everything that opens up to you postgame, you can have a mon ready for wi-fi battles in like, half an hour as opposed to for-friggin'-ever if you try to do it as you go through the main storyline. I've always thought of my ingame team as the old guard, training up the rookies who will eventually surpass them and go on to do greater things.
I'm kind of silly like that.
I personally treat Pokemon's ingame and the metagame as two separate things. Ingame is truly a different beast. While you probably can't ever have that true sense of ignorance that comes from not knowing about things like IVs, natures, and EVs once you find out about them, it's not impossible to have an enjoyable casual playthrough of the game. There's a certain charm in your ingame team - they're not perfect, but they got the job done. If you have friends who play Pokemon as well, chances are you've got at least one who doesn't really understand how all this stuff works, and it's not very fun curbstomping them when you have a team that outclasses theirs in every single way. Don't think of yourself as wasting EVs - after all, it's not like there's only a finite amount of EVs available in the game.
As for what you should do for Black 2, I personally find a pure run, just catching what you find and going from there, would be the most fun for a first playthrough. It's not like you can only play the game once and you're done forever! If you want to import a metagame viable team, go ahead, but don't worry that your Ferroseed is getting special attack EVs - you can erase them later with berries and retrain again in a small amount of time.
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