Hi Mohamed,
tI do not see your eye diagram weird. if you mean you want to improve the results accuracy just you have to send more bits (i.e. increase sequence length from the global parameters of the project). But if you want to improve the system performance itself, you can decrease the propagating channel length, decrease the dispersion effect, increase the the power of the received signals toward the photodetector,…so on.
hope this helps,
thanks
Mohamed Abouseif