you can replace disc drive with sata ssd, and make the console use sata instead of the onboard emmc (gotta cut a trace on the board, you dont need defuse anymore you can use isfshax) but you break vWii when you do this. I dont know if the adapters to replace disc drive with ssd are available yet though. If you care about vWii this isn't worth it, keep the disc drive and use nand-aid or rednand if you want bigger internal storage.
For gamepad range I think you can do this
https://gbatemp.net/threads/wii-u-wireless-controller-extender-hack.378742/
gamecube ports and ethernet jack I guess you could theoretically tear down the usb adapters, remove the usb ports at the back of the console, and wire the usb adapters directly to the board. then have the ethernet port stick out the back and the gamecube ports at the front. or if your case is bigger than the original Wii U, you dont even need to remove the usb ports, you can just plug the adapters in inside the case and have the ports facing out the back/front. you'd save a bunch of space if you removed the usb ports and wired the adapters directly to the board in their place though. one potential problem is that the ssd might get in the way of the gamecube controller ports, you'd need to account for that when designing your new case
if you still want ssd, I see no reason why it couldnt be wired to the board via usb and kept inside the case as well. you'd probably need to leave an extra port at the back for power though, if your ssd needs wall power to function (wouldnt be a big deal I think, instead of 1 wall plug for the console you'd just have two.)
but then again, that's a lot of stuff to fit inside a Wii U case, so your redesigned case would need to be bigger to account for this.
gamepad idk, there's no reason why you couldnt just put the internals into a nicer casing and replace the original analog sticks, but "an upscaling chip" would require pretty extensive modifications to the hardware for it to actually be used, and I don't know if the work for this has been done yet
