Kind of depends on the bike, don't you think? My ZX12R works perfectly with the FI, and it also has a Power Commander III and a full Akrapovic system. My ZRX works perfectly with carbs!
Harleys, in my experience, are MUCH better with the FI.
Having the mechanical ability of a footstool, I try to do as much of my maintenance as possible with a checkbook. It took me 30 years to discover that I save both money and time this way. With that background, any system that requires no maintenance is good for me.
As an example, I adjusted the chain on my ZRX today, and it was a comedy of errors. You would not believe anyone could make a 45 second job so difficult!
I owned a 1977 Yamaha XS750 triple for 22 years, and loved it. It always ran perfectly, and I never touched the carbs over 58,000 miles. A friend of mine just bought the same bike from the second owner and needed to spend some time on it, because the guy had "adjusted" the carbs so that it would hardly run.
In coming years, as computers continue to get more complex, and cheaper, I think all bikes will have FI, and they will all run perfectly. Garage mechanics everywhere will then complain that they cannot "improve" their bikes like in the good old days.
I have been riding for 35 years and the sum total of all of these experiences is that 1.) These ARE the good old days and 2.) Most people who work on their motorcycles really should not!
One caveat - I now work for a dealer, and I get to see my bike worked on and I know who is doing the work - life is good.
As for me, soap and water and wax are the only mechanical operations I enjoy - and the only ones I can do without endangering myself and the bike.
Yours in humility,