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If you have like minded individuals, online franchise is very fun. But in an online franchise it's still about competition, so in practice you have less room to experiment- not only because, for example, running an offense with a 90% passing ratio would probably cause you to lose as the opponents adjust, but also because such things are likely against the rules of your sim league Not only that, you can only control 1 team.
So, in a nutshell, I prefer both for different reasons, and use both for different play styles. Nothing beats going against true intelligence with a sim minded opponent, but there are limitations with online franchise due to league rules and the simple fact that you only can control one team.
Note: it is possible to find an online league that takes great pains to eliminate cheese, which seems to be the number one gripe. I get the feeling mamy people here have never played in a committed sim league.