If you could hotkey the extra champions it wouldn't be so bad, but right now using extra champions is to tedious to be 'fun'
Ctrl-H switches directly to each Champion - it just also switches the HUD to that player. Personally, I rarely split multiple Champions into more than 1 or 2 groups, so I can shortcut to Player 1's Champion and get all of them the vast majority of the time. The rest of the time, I use Ctrl-H or the Galaxy Map on either the Champions filter, or the Broad Search -> Shadow Ships filter.
While it would be nice to be able to put other Champions in a group, I don't find it difficult to work around.
Same thing with designs. As Player 1 create them, and save to disk. With Player 2+, just hit the "Load Settings from Disk" button, and it'll auto-load all the designs. Do it once at the start of the game, and you're done for the next 20 hours.