Its the whole "well it works for the Champions League so why not here" line of thinking that I find annoying...
What they should have done is top 11 in each.
#1 goes to a semi
#2 & 3 play to see who goes to a semi or who drops to a group
10 & 11 play to see who goes to a group
Loser of 2 & 3
Winner of 10 & 11
6
7
4
5
8
9