Even with the release of the new console it will be a long time before any of us see a modded controller for the next gen consoles. Companies will be spending so much money in tearing apart these new controllers to see what they can actually do with them. Not to mention we will have to wait for the right titles to come out to use mods on and even then we will have to see what exploits if any are availible to us. The technology put into these new controllers will probley be a modding nightmare to manually mod. I wouldent be supprised if internal mods are done away with all together. I think the new technology will be in external usb mods. Who really knows what the future holds for mods. Im just speculating my opinion on the matter and thats all it is, a opinion.
On Sony's side, I'm not exactly sure of their motivation for not allowing older controllers to connect. It may be something similar to what XBOX is doing, sorry to compare it to XBOX but here goes:
On XBOX, they want total control over third-party accessories. They sued Datel over memory sticks, then turned around and sued Datel over their unlicensed controllers. In the case of the unlicensed controller, Datel hacked Microsoft's authentication protocol required to connect a controller to the XBOX360 console. Once it's hacked, there's no unhacking. In order to close this loophole on XBOX "720" Microsoft has to disable all previous controllers from XBOX 360 from working on the new console. Essentially they will be coming out with a new "Secure" protocol for locking down their console in terms of allowing third parties to connect accessories.
Apple does the same thing - they even put encryption authentication chips into their fricking charging cables to force you to pay $30 for a charger cable that should only cost you $2.99.
So it's possible Sony has similar reasoning of wanting to cut down on third party accessories. Another possible motivation is that the only way to get users to try the "ps move" is to integrate it with the controller and "force" you to use it. Also the touchpad in my opinion is stupid but again, the only way to make you try it is to put it on all their controllers. I suspect that later down the line about a year after release, Sony will probably release an official dual shock controller without the touch pad. Look at Wii U - they released the Pro controller because they realized that not everybody is in love with a big giant screen on their gamepad...