There are a few variables that will determine the future for flydubai. They will not kanabalize EK's routes if the introduction of flydubai starts hurting EK on a route. They will try and serve 'underserved and secondary' markets combined with a few big markets where there is obviously enough for multiple carriers.
flydubai already operates to 40+ destinations together with EK. Many European countries are looking to block/slow down the M.E. carriers uprising so they may block flydubai coming on their turf too. So they could be looking east at deeper into Russia and maybe China and Thailand etc. West bound Africa looks very promising too.
It all depends on billateral rights and goverments. Maybe even a base outside of DXB as a stepping stone to places further away.