The upside is that the aircraft on regional flights can be the same as on long haul (e.g., A380, B777 three class) and it's full service. The downside is that EK has an exclusively wide body fleet so loading and unloading can take more time than the actual flight to DOH or BAH. On real short haul routes (DOH, BAH, RUH and maybe even KWI) FlyDubai's 737 fleet can be more efficient especially as as they fly out of T2, which is small and easy to get in/out of. Downside is that FlyDubai runs a Low Cost model (comparable to EasyJet) although they have added Personal TV in Y and recently introduced a decent Business class for short haul.
...and get your E-Gate card as soon as your visa clears.