Ok, This is my OPINION, so take it with a grain of salt...
Carburetor:
+: Cheaper, easier to troubleshoot, no wiring (unless you have electric choke), fairly easy to get parts.
- : More maintenance, won't correct mixture for different fuel blends, Ethanol blends can corrode aluminum parts.
Fuel Injection:
+: Fairly maintenance free, can automatically adjust for different fuel blends.
- : Expensive, Everything is electric, can be a pain to troubleshoot, Fuel system has to be changed to work with fuel injection (higher pressure pump, possibly a return line to tank), parts will be dependant on system (and possibly sourced from manufacturer), exhaust may have to modified for O2 sensors.
Hope this helps, I'm sure others will chime in.