Like with trading custom stages, you're supposed to be able to trade gear between versions in a future update. Why the hell they didn't have that available from the start is anybody's guess.
I honestly only use equipment in Smash Run. Auto-Heal is pretty useful there, as is the Crash Run ability.
Hey guys, you remember "CD Factories" from Brawl? Well, that's not really all that useful anymore, since Sandbag doesn't drop CDs anymore; but there is one thing in the game that still drops CDs quite frequently, and that's Mew.
I've seen some suggestions online that the easiest way to unlock CDs is to turn off all items but Master Balls, set items to high, set stock to 99, and fight a level 1 opponent using only the Master Balls. This nets you usually on average about 6-8 CDs on average.
This is not bad, but my problem is that you don't have much control over when you want to stop the match. If you end the match early you don't get to keep any of the CDs you collected, so you're stuck playing until your opponent runs out of stock. Also since you do have an opponent dicking around with the pokeballs as well, you actually have to pay attention to a small degree.
So what I did was I built a simple custom stage that looks like this:
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attachment=4932]
(click to expand)
Knocking your opponent into the barrels causes them to fire back and forth infinitely and also makes them completely immune to any Pokemon effects. You can then just set your stock to 1, and use Master Balls at your leisure, paying as little attention as you wish since you are in no danger, meaning you can just use your Gamepad screen while you watch TV or surf the web. When you're done just throw yourself into the abyss, ending the fight and collect your reward.
This trick should also work for any challenges that require you to play Smash mode for so many hours (are there any like that in this version? I haven't even looked).
It might technically be faster to unlock CDs via Master Orders challenges, I'm not really sure, but at least this method doesn't really demand your attention.