Maybe even 2 clubs for Croatia and other smaller countries could be too much. You can't rank Spain same as Croatia because the difference in number of players, especially quality ones is too big. Countries like Spain, Germany, Italy, England, France maybe Portugal should have one club more than others Imo. Otherwise, the difference in quality of teams will be huge.
Your vision makes sense, but it's simply impossible for country with 4,5 millions people to become so powerfull in football, law of large numbers doesn't allow it.
PS @Jason, hope Slovenia counts in Central European/Russian Countries, we need GK.