In a situation where only pre-approved customizations are allowed for specific characters for the purpose of balancing, I can't imagine it adding more than 15 seconds to any given match. But yeah, an amiibo being able to store custom movesets, as in Brawl with the wii remote, would be ideal.
Pre-approved customizations seems limiting and it would probably take a LONG time for the community to figure out which, if any, are OP. As for how long it take to pick movesets, we have no idea what the interface to do so looks like. Do you do it off the character select screen? Do you have to go into a different menu? Is is something both players can do at the same time or do they have to take turns? How long does a player have to pick their moveset? If they want to counterpick (make changes on how the last game went) how long do they get? Lots of variables to consider.
Overall, it depends how forward thinking Sakurai was with this feature and if he even envisioned it would be something tournament players would even want to use. It could turn out to be pretty fun though. Picking grooves, assists, arcanas, etc. has always been a fun way to add depth to your fighting games. I'm just hoping custom movesets in Smash are better implemented than Gems were in SFxT (bleh).