Nintendo won't find a way to stop hacking because they don't care about competitive battling in general. They only care about selling games (which I don't like on one hand, but can't blame them for on the other hand).
Hacking is all about how you handle it. A lot of people have an intolerance for hackers not necessarily because of time spent or the handheld metagame, but because there are idiots out there that hack all 999 pokemon or Pokemon with illegal moves/traits or whatever, and nobody wants to play against that garbage.
From what I've gathered from previous dicussions here and the mods is that hacking is defined here as using any cheating device outside of the game to enhance the creation of a pokemon. This includes parents, egg time, or anything else that could make the hatched pokemon you're actually going to use better than it normally would be without such a device.
Personally, whenever I fight somebody over Wi-Fi with my DS, I assume that their pokemon has perfect IV's and is EV trained in some way (Assuming I play on Smogon). The focus of this website is competitive battling as opposed to the handheld metagame.
My personal stance on the matter aside, if your going to hack (in other words, if you do anything that falls under the definition of hacking that I put in this post), there are courteous ways to do it on Smogon that are generally accepted by the majority of players here...
1. Don't ever ever ever ever offer a hacked pokemon for trade. There's just no reason for it. Hack it yourself if your just going to trade a hacked pokemon. Certain pokemon (Deoxys, Arceus, Dakrai) and clones obtained via AR are generally exceptions, but you should still note that were obtained with the use of a cheating device, because some people don't want to trade for them at all.
2. If you're battling with sharked/ARed pokemon, you should notify your opponent. It's as easy as putting that you're an AR user in your sig or telling your opponent that the pokemon you are using is ARed or sharked. This applies even if only 1 pokemon on your team is hacked. Most people won't turn down a match if your stuff is hacked and you tell them beforehand. It's likely someone who will turn you down for this isn't someone you want to play anyway.
3. Don't play people with illegal shit (meaning stuff that can't be obtained in the game). It's completely BS, most people here will catch you, it does get you banned from here, and it gives credible hackers a bad name. Do careful research on legal breeding combinations, EV combinations, Natures, Abilities, and the like before you make your teams. There's so much information out there that there's no excuse for illegal combinations.
4. Don't enter hacked pokemon in tournaments that explicitly exclude hacking. This includes official Nintendo events, all tournament battles here on Smogon, and any other tournaments you run into where hacking is not allowed. You're just asking for trouble by doing this. This is a rule that is expressed in most tournament settings (because of the metagame), although my personal tournaments don't because I've modified the rules to make the playing field more level whether or not people hack and I only have a PBR to use in my area, but that's enough about my personal stuff.
My point is that if you're going to hack, don't be an idiot about it and most people won't care as long as it's in a casual battle setting.