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I don't think there's something wrong with allowing teams financed by a single source into the UEFA really, it doesn't tarnish the reputation of the league in the first place, it allows more people to enjoy the game and more players to show their prowess, and most of all, it's going to keep the game of football alive!
That's quite a naive thinking. How do you think football fans would look at the competition between two sworn rivals and a competition between two sister clubs? The intensity of the game would be different at the very least. Another thing is that there will always be rumors of a rigged game that would affect the league's reputation. They don't want any of that so it's better to avoid it from ever happening.