It would be nice to have more options regarding the groups stage in Cups.
Particularly the 3-player groups bug me. They aren't so fun in groups stage and you'll end up with a massive knockout phase (with quite a big chance of facing an elite player in the very first round).
I know that if you remove the 3-player option it'll be hard to get the right number of players in (no more 6,12,24,48 as correct numbers to start a cup with). That's why I'm hoping to see either 6-player groups as alternative (it covers exactly those numbers) or make the group-count completely up to a mod's choice (groups of anywhere between 3 and (i dunno) 16? players). Same with the # of players to advance to k/o stage.
That way you can even make 24-player tourneys with 4 people in each group (1 and 2 advance + the best 4 players in 3rd spot). As odd as that may sound, it was the system used in the WC Football until a few years ago.
It would give MOD's a lot more options; decrease waiting-times (for the right number of sign-ups) and allow people more creativity in hosting their cup. For example, clans would be able to make a cup with 1 group of 12 players (all clan members) and at the end of the month advance the first 4 into k/o. That way they have their own little inner-clan league on TUS.
I think it would make a lot of people happy.
And maybe a final suggestion: allow people to sign up for a cup after it has already started, as to create a reserve list of players incase one drops out or fails to meet a deadline.