Easy to understand, hard to determine the reasoning for the crappy cup payout.
I am now level 4 where CL pays $8.04M and the Cup pays $3.71M for winning the finals.
I would say that I had a very high quality team for a non-token buyer and easily out-qualitied most of my opponents throughout the season.
My brothers account is level 3 where he is almost the same quality as me (27) so he is playing in the same level cup with the prize for winning being $3.71M but his CL winner gets $4.82M
So in both cases, CL gets significantly more than Cup.
I would agree with you that the cup money is bases on the quality of the opposition. BUT for the average non-token buying manager, which would be ALOT of managers, the cup money is crap compared to the CL money because of the lack of quality.
At the end of the day, CL money is normally much better and you face lower quality opponents.