To be more specifiic, said NPC is in the Pokemon Center of the battle maison.

This is a bit worrying (emphasis mine):

Source: http://www.serebii.net/news/2015/04-August-2015.shtml
Original announcement in Japanese: http://3ds.pokemon-gl.com/informatio...6-ddc42774ccc8

Okay... What are Rating battles and Battle Competions?

Hmmm. How do I put this? Think of it as Pokemon's version of matchmaking. Having ranked and unranked battles plus competitions that happen every once in a while that gives out either a pokemon, item, Pokémiles, or points for VGC (Pokemon's equivalent of MLG live events.)

And if my battling just involves passersby and you lot through the PSS?

Those don't count as Ranked Battles/Battle Competitions. Even casual battling on Battle Spot doesn't count. To be ranked you actually need to sign up for it.

And thus my worry dissipates.

Until you realize that they still intend on having some kind of harsher punishment for multiple offenders.

Yes, for the thing you have to sign up for.

You don't have to sign up for PSS and there is no mention of PSS.

My main concern is not for the fact that this emphasises Rating Battles/Battle Competitions. It's that I can't see how it will be possible to implement a strict penalties system without essentially punishing large swathes of innocent players.

Anytime you log online and trade, be it with GTS, or through Wonder Trade, you have already exposed yourself to the risk of getting hacked Pokemon. There is absolutely no way to tell the difference between a hacked but legal Pokemon, and a legitimate Pokemon. Even strict definitions of legitimate have to concede that somewhere down the Pokemon's breeding line there is a possibility that some hacking was involved in its ancestor.

There are many, many casual players out there, delighted that they suddenly got a lvl 100 shiny Rayquaza in Wonder Trade, who might not suspect or even care that their Pokemon have been hacked. I got a Cobalion once, I haven't bothered to check if it could be legit or not. Should innocent people be punished for the failings of a system along with hackers? What if this guy wants to use his Rayquaza on a Ranked Battle?

The only way to be entirely free of hacking is to never trade Pokemon, which effectively ruins a major point of the games.