Well, with an integrated hardware component, the controller input is sent over a dedicated hardware bus.  All you have to do is read from a specific memory address and find out what buttons are being pushed at the current time.

But the Circle Pad Pro uses IR light to send controls to the IR port.  Now depending on how much work the IR port is doing, you may need to read from it fast enough to decode the digital pulses being sent.  It's like decoding Morse code.  You have to pay attention long enough to hear all the pulses and the silences, then determine which pulses were dots, which were dashes, which pauses meant next letter, next word, new signal, and so on.

So you have to dedicate enough CPU type to checking the IR input and then decoding that into controller button presses and then pass that along to the control input subroutines.  That's why it gets so much more difficult than an integrated button.

Wait, it takes 5% of the 3DS's processing power to accommodate the Circle Pad Pro? Yeesh, I didn't expect  it would take no more then like 2% to handle it.

I wouldn't be surprised if the IR receiver is really dump and the poll rate has to be really high to be reliable, especially for a game that needs a high enough poll rate to have super low input latency like a fighting game.

No circle pad pro support,
No Ice Climbers,
Fox only,
Final Destination

Super Smash Bros: For the Glory of 3DS
Only the Hardcore step in here.

You forgot "no transformations", but I do find myself playing the world's tiniest violin...

Based on what logic are these supposed to be words we wouldn't want to hear?? I can't speak for everyone,  but I'm more than happy to hear there was a rational explanation.