If you mention both nunchuck and classic controller (supposing they're original) are working fine, but wiimotion+ fades along the internal IR wiimote sensor, then something inside must have been fried, say, the internal wiimote's IR. You could always try another sensor bar just in case, or another wiimote on the same sensor bar.
Maybe there are guides in google which may help you replacing the internal wiimote IR led...
edit: or a blown capacitor (the one dedicated to feed with continuous voltage a target hardware)
Yeah, I charge the wiimote, and throw in fresh batteries, and the motion sensoring is fine, the lights on the wiimote fade to nothing, and that's when I start getting IR problems, the button presses work fine, the remote syncs ok, I put it back on the induction charger until the light indicator is green, and bang, it works ok, but the lights always fade, even when the wiimote has full power, and the IR controls begin the fudge. It's also worth noting that I CAN play Classic Controller only games without issue, it's just that motion sensing that screws up.
The way the charger works is that it pumps power into the battery pack when it sits ontop of the charging plate, but the battery pack needs to be IN the wiimote, and the wiimote sits ontop of it. I voltage surge from the induction charger to the Wiimote might've fried something inside, which is what I'm thinking might've happened, since the offending batterypack no longer works, but the second battery pack does, but with the fading wii lights, leading to motion control/cursor disappearing issues.
This is what it looks like.
I've recently had issues with it overcharging, or stating that the pack was charged, BEFORE it was fully charged.