The past 9 months or so I've been working on an FE with an aftermarket FI system installed. In the FWIW column I've observed the following.
If the engine was originally designed with a FI there are a lot of tuners and information on tuning the system available and dealing with it can be RELATIVELY easy.
If the engine wasn't originally designed for FI it can run the gamut from a real can of worms to relative ease. Tuners and information on the system become much more rare. Finding a tuner who's knowledgeable about the system can be a major undertaking but if you find one he or she is worth his or her weight in gold. Tuning a "non standard" system yourself requires an extremely steep learning curve. It can be done but it can be a struggle.
Unlike a carb an FI system is incorporating several different disciplines which, in general, aren't commonly known.
On the plus side a well tuned FI engine is a real pleasure to drive. Most of the systems have enough latitude in their make up to correct for minor anomalies that come up in day to day operation and are seamless in their corrections. They will compensate for differences in atmospheric pressure and temperatures without missing a beat and remain running at their most efficient level. The ability to have multiple tunes that you can switch to on demand is also a plus.
All in all the FI hasn't really eliminated the old "shade tree mechanic" but it has forced him to move to a different tree.
Both camps have their champions and their detractors. What I've found is that, as with anything else, knowledge is king both in deciding if you want to go to an FI system in the first place and working with it after you've got it.
If you do decide to go with a FI system REALLY do your homework. Find someone with the system that you're looking at and really pick their brains about the care and feeding of it. Going in without a solid foundation can lead to a lot of disappointment and unnecessary expense. If you have someone else tune for you it can be expensive up front but if you opt to do it yourself dust off your reading glasses and be prepared to burn some midnight
oil.
Modern FI systems have come a really long way in their capabilities but, relatively speaking, it's still a very young discipline. Before you start make sure the engine is as mechanically sound as possible. While a something as simple as a vacuum leak isn't a big deal is a normally aspirated engine it can have you chasing your tail with a FI system if you don't know it's there.
Not taking sides pro or con on the FI, just observations from where I'm sitting.
DonC