Ok so every pokemon you catch will be "useless" as the "best" traits/shiny/nature/ev's pokemon will be cloned.
So? The Pokémon that are EV traied and what not are the superior ones. Is that a problem?
Meaning that :
1)Breeding is useless , you can just trade any pokemon with whatever stats/traits/natures/ev's will be cloned like hell meaning that breeding is useless as you can just trade them for one of your own pokemon.
Yes, breeding will become obsolete, except for D/P Pokémon.... because you can't clone in D/P.
2)Catching pokemon is useless , see 1.
Good, now I can save my money for Vitamins, as opposed to PokéBalls.
3)Legendarys/rare pokemons will be cloned like mad , meaning that they won't have any tradevalue anymore and soon everything exept PERHAPS a shiny will be worthless.(screwing up every trading possibility for the game and thus ruining the gameplay)
I fail to see how this ruins gameplay. If you don't want to get rare Pokémon via trades then..... don't trade. -_-
4)With every pokemon with whatever stats being available for nearly nothing as they'll be mass produced , you'll never find a "weaker" pokemon.Thats really annoying if your trying to train/breed your pokemon properly which is in my eyes the biggest part of the endgame.
Get a clones Pokémon, breed it to get a "weaker" version. OR, GOD FORBID..... you catch one yourself.
5)I can continue about this...Basicly it all comes down to this, "If you play without cloning , you'll play longer as you'll have more work with breeding and training , if you clone all your pokemon and trade them for other clones , you'll quit playing soon as all thats left is battleling vs other people with exactly the same pokemon"(just look at netbattle if you don't believe me, i see a total of 25-30 diffirent pokemon being used exept by the very few UU players)
You obviously don't Netbattle often, because the metagame is nothing like that.