For what it's worth, I have a carb'd Bonnie and an EFI Sportster. There are pros and cons with both (bearing in mind we're also talking different bikes). But different bikes aside, here's what I'd say:
EFI
Slightly better fuel consumption
Factory set to run very lean at 14.7:1 apparently (this is for the Sportster, so check the Thrux factory setup)
More 'modular' when it comes to changing things e.g. you can change fuel management components (not cheap) and settings, depending on the setup. Think you can also get different O2 sensor leads to make it run richer.
Easier to set a flatter air-fuel ratio curve throughout the rev range
Will adapt to different ambient conditions
Not really user serviceable
Carburetor
Old school technology - attractive for some, a pain for others
Easier to work on and service yourself
Cheaper to work on yourself - jets are pretty cheap
Well established and reliable
25 minutes to change jets if you want to do this from season to season i.e. if your climate changes severely affect your fuelling
If I had to make a choice it'd be difficult, but I'd probably still opt for carbs, personally. That's to do with the pros listed above, but also because I ride a Triumph mainly for nostalgia/ sense of authenticity rather than performance. I'd go for EFI on a performance machine.