Given the current amount of teams in the game, this would be my preferred Master League setup:
6 domestic leagues, of 16 teams each:
- "Britain" - 14 English teams, Rangers and Celtic
- "Iberia" - 13 Spanish teams, Porto, Benfica and Sporting Lisbon
- "Italia" - 16 Italian teams
- "Benelux" (Holland/Belgium) - 14 Dutch teams, Anderlecht and Club Brugge
- "France" - 16 French teams
- "Europe" - made up of 16 clubs from 'other' European countries like Greece, Turkey, Russia, Scandinavia etc
Why 16 teams only? Because that way, the bottom 3 per league can still get relegated and the clubs not in the league can still get promoted the following year (anyone remember FIFA 2001?). This way you get to face new teams every season, whereas if it were 20 teams, in some leagues like France and Italy, no teams would be able to get relegated. The only issue with the above is what happens if your team gets relegated, because there would be no Division 2 to play in...i guess that scenario could be either "Game Over", or your team is forced to spend the next season in oblivion before winning auto-promotion for the following year or just let the user pick a new team in the same ML.
The other advantage of 16 teams is that in the domestic cup no teams would have byes at any point of the competition, whereas in a 20 team league, 12 teams would get no action in the first round. Of course this implies that those other teams (the ones not in your current season but may get promoted next season) do NOT participate at all.
As for WEFA competitions, in my format i'd set it up like this:
WEFA Champions League
Top 4 per league automatically qualify for the group stage, which is 6 groups of 4. Only the group winners progress to the quarter finals, along with the top two runners-up to make 8 teams (a la the old real life UCL format which ended in 1999). And FFS Konami, code it so that i don't face the same domestic teams in my group again
WEFA Cup
The domestic cup winners along with the teams that finished 5-7 in each each league (or 5-8 in the case the domestic cup winner finished in the top 4 too) compete in the first round. 24 teams, knockout, reduced to 12 teams in the second round. Then these 12 are joined by the 4 other lower-ranked runners-up in the WEFA CL group stage to make it a second round of 16 teams. Then it becomes a standard KO format up until the final.