Thank you very much for your input and advice.
Our major focus will be on the Engine and Map/Game editor which we will then be used to develop the 2D version and many other projects. We are hoping that, because the project wont rely on the ceation of the 2D version of OOT, that it will be easier to finally come to an end result as you are completely correct. The struggle for 1:1 is almost impossible. Instead, we we would like to aim for a similar gameplay feel. One of the other guys working on this said that when it finally comes to creating the OOT 2D version, we should replace the 3D aspects with the 2D equivilent, not try to replicate them.
And of course we see no issue in altering and improving on the original game (Hyrule field is a good example, as is the Water temple, almost impossible to replicate in 2D and still make it enjoyable I would say).
Thanks again for your advice and input. We know it is no small task but appreciate your encouragement.
The OOT2D Team