Actually I think this is one of the things that are quite balanced in the game. Are you competing for the top 4 in the League, you'll probably have a strong team, competing for the CL victory as well. Are you just hanging on in the middle/bottom of the League, chances are you're a lower quality team and be more competitive in the Cup. I know most managers have the (natural) urge to get your quality up as high as possible, and would be in the 1st catagory. Sadly some also have the urge to complain about anything if they can't win the treble, but forget to see that for a large group of players the format works quite well. The only real downside is when you lose to abandoned teams, if they could only filter these teams out.

The seeding of teams in the several formats are one of the few things Nordeus explains. There's also a choice to be made that influences the seedings greatly. There is a very wide bandwith in price-quality in players. You can have 3* players being twice as expensive then his 5* counterpart. Use these 2 givens to your advantage. IMO it's all about balancing the 2, you'ld be surprised how flexible the game is. I find that these decisions ultimatley have a far greater impact in the game then tactics, formations and matchattendance to name a few.