Team battles in tournaments with ditto's I'm sure the community will ensure that if you pick a team color you will also need to change your characters color to match it.
So blue teams will still need to keep their characters blue. At most its a minor inconvenience. For casual play though this is good, as now you're no longer forced to go with colors for your team that might look bad on your character (pink pit I'm looking at you)
Besides I think this might be a 3DS only feature, as it seems like the outlines are anyhow, and I doubt the 3DS one will seriously take off for competitive play like the wii U version.
And even if you can still pick any color on the wii U version as well, I'm betting the arrow that is hovering over your head(or any names) will always be there and allow most players to know which character is which. on top fo that, again, the community itself will still make sure that in teams you make sure your characters change their costumes to the same color as your team.
So I dont' see any big issues with this up date