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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?
To be fair I think fans wouldn’t care too much if two teams were from the same ownership in a sense that they would still be loyal to the one team they really represent and they wouldn’t magically care about the other team even if they are a “sister team”.
With this said, if one team gets disadvantaged in favor of the other, fans would immediately call it rigged even if it isn’t. The bias and reputation would be too much to argue otherwise. There is also a real possibility that the owner would try to sacrifice the other just to make the other team win. They might not do it but they can and that is what a lot of people, not just fans but also commentators, sport analysts, journalists and the general public, would think and imply.