I think you need to flesh out your plan a little more to get to the best answer. I've been down this road before, and it can be a long one. You need to make the right choice for the right reasons.
I bought a Pectel T2 engine management system. You probably haven't heard of it before, it's European and they typically only do professional motorsports stuff. With the T2 they were "slumming it" and offering something affordable. I went with it largely because they had a plug and play wiring harness that interfaced with the factory engine wiring harness. Also it was developed around my engine, and working basemaps were available. The system is incredible, but their support was terrible and little other support was available. It would probably still be sitting in a box if it wasn't reasonably easy to use and I was working in Ford Powertrain at the time and had access to training.
Are you going to be doing the programming yourself, or paying a "tuner"? If doing it yourself, the most important things will be ease of use, and access to help, such as forums, good manuals, etc. If paying a tuner, a key thing will be to use something he's familiar with already. No point paying him to learn a new system. And a key point about tuners... just because a guy owns a dyno, don't assume it means he has any idea what he's doing. Some tuners can barely get a car running well enough that it can idle from the trailer to their spot on the carpet. Others only know how to make them idle, or go full throttle (for about 10-15 seconds). You need to find a shop who knows how to make an engine run through the full spectrum of load and RPM, in any weather. I can only advise you to look for a shop that has a reputation for doing circuit racing cars. If all they've done is drag cars, or magazine cars... probably not going to work for you.
What are your goals? Do you just want to replace a carb so that it starts better and works at altitude? Or do you want to maximize torque and efficiency? A simple throttlebody system is a little simpler mechanically, but I don't think it's really much easier than a sequential multipoint system in terms of the programming.
I'd suggest maybe looking into a custom setup based on a Ford EEC computer. About 1 year after I did the Pectel, Ford completely opened up the architecture of this computer system and there are tons of good programmers on the market for them. They are easy to program, robust, and surprisingly high performance.
I don't care about fuel economy too much.
