A suggestion...

I quite like Scott's 3rd suggestion and James' idea. However, I have another suggestion to throw into the mix:

The cup can progress over 2 seasons, much like the World Hattrick Cup does now.

First season is a ladder style tournament event. Each team would be awarded points for each match they play:

1) 3 points for a win (I will assume cup rules throughout so no draws)
2) 1 point for every goal scored in normal time plus 1 point for a golden goal.
3) 1 point for every position in the ladder the loser is above the winning team.

Example: Position 1 loses 4-2 to position 4. Position 1 gets 2 points for the goals they scored. Position 4 gets 3 for the win, 4 for the goals and 3 'handicap' points, totalling 10 points.

Any team can challenge any other team and so active teams get an advantage simply by playing (as long as they don't lose by scoring no goals).

The week that starts qualifying matches will be determined by the week after all teams have been knocked out of their relevant national cup.

Season 2 will take the top 4 teams and play them in a 6 week round robin to find the top team. The 8 'losers' will play a 6 week 2 leg straight knockout.

Well this is just a work in progress but you get the idea?