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DownTheDrain:
Well, that's the Sandbox working. I mean, people are totally free to ignore Tony and the main story as long as they want, as long as they don't run into it by accident. If there would be a better possibility to chose, then I'd have no issue with that to be honest and to some degree it'll always be up to the player to give himself a good experience.
I mean, in the end main story stuff is still not really heavy or threatening. All of these antagonists like the mobs, Rump, Kim, etc. are somewhat cartoonish (like you imagine most of these Disney/Warner Bros. villians) and seem pretty harmless in general.