If you're suggesting it as a way for Ganondorf to be sealed in the past as well as the future, this causes some problems, messing up the timeline for Wind Waker and A Link to the Past. The future events of OoT HAVE to happen, because they are recollected in both WW and ALttP.
Not ALttP, unless you believe the events of OoT are the Imprisoning War. (Let's face it, OoT isn't much of a war is it? Sure, Ganondorf wages war against Hyrule Castle, but that's about it. There isn't some big war to seal him back in and the Master Sword wasn't forged in the events of OoT as a response to Ganondorf as stated in the Legend of the Imprisoning War.
Also, there are no paradoxes. It seems like there are but after looking closely I can't spot any except some possible gameplay-related ones.
Which are still paradoxes that really mess things up.
BTW, would you consider Link returning to the past a paradox? His presence there would inevitably result in a paradox, because, he wouldn't just sit back and let Ganondorf take over and it would seem from the beginning of MM that Ganondorf hasn't really attacked Hyrule or taken it over.
This means that the future events of OoT cannot happen because Ganondorf hasn't taken over Hyrule, which means that Link would never have defeated Ganondorf in the future in the first place, so he wouldn't have memories of his future.