I would consider the Arabian Airpass. It is US$ 100 rtn ++ to MCT on EK out of DXB and best of all you can check in all the way through. If I am not mistaken there is a 0200 flight out of DXB to MCT.
I would much prefer that then to have to get your bags, get out of the airport, take a cab to Sharjah for a flight and then have to do it again on the return. You would spend the difference on cabs and accommodation anyway.