I have experience with all 3 systems to one degree or another. I assisted in installing a MSD system some years ago, currently have a FAST EZ system (harness and controller with a F&B 6 pack), a Holley HP system (harness, controller and hall effect distributor with a F&B BB 6 pack), a Fitech Go Street 400 on a 56 Desoto Hemi in my 52 B3B pickup, and am currently installing a Fitech "Tripower" in a 69 Plymouth wagon for a guy.
I have talked to both Holley and Fitech directly (at shows) and through their customer service lines. I will say that in my experience, they were pretty similar. Talking to Fitech feels more like calling a small shop where you kind of need to talk to the one or two right guys to get the information you want (depending on what it is you want), however once you got the right guy you are good. Subsequently talking to Holley seemed more like calling a corporation, they had more general information but if you wanted to dig down it is a problem and again you will need to find the "right" guy to get real detailed information.
As far as the actual systems go;
The MSD that I worked with (perhaps they have gotten better) did not impress me all that much. It was marketed as a "returnless" system but in bold print on the first page of the instructions it stated that while you "could" run it returnless you really needed a return line. The system worked ok for the most part but seemed clunky and kind of like something someone built in their garage.
The fitech Go Street system is well made overall, super simple to install and has worked exceptionally well. Has like 4 wires to hook up (along with a the right fuel system and an O2 sensor). It definitely has learned and I am very happy with it. I am running a Tanks Inc. tank and pump for this application with a return line and vent.
The Holley system I have (HP) was much more complicated than either the MSD or the Fitech, however it does control spark and fuel which is very nice. The HP computer is fairly large so finding a spot for it can be a challenge. In my case I put it into a 70 Challenger RT and I put the computer inside of the drivers side fender high up on top of the brace. It has water tight seals and thus far as been good. I am running a Tanks Inc. tank and pump with this car as well as a vent.
The FAST system I have is the EZ 1.0 which I bought many years ago and finally installed it last year with my F&B 6 pack. It is a relatively simple system but does have a decent sized harness for it. The controller is pretty small so mounting it isn't that much of an issue (mine is mounted behind my modified glove box. In this application I am running a modified stock gas tank with an external Walbro 255 lph pump which is mounted in the passenger side wheel well on the frame rail.
All of these systems essentially do the same thing and pretty much operate in the same way. The main differences really come down to pricing, looks and application. They will work pretty much equally if you install them on something you do not intend to modify, however if you intend to keep the system forever and build power over time then you need to look at each very closely; none of them are really up-gradable but will support a HP range and so long as you stay in there your are doing ok, but if you exceed that range you are going to be looking for something else to support it.
IMO it comes down to what you like because pretty much all of the self learn only systems are the same (generally). I am very happy with my Fitech system but love the tunability of my Holley system. The FAST system is pretty much the same as my Fitech system but there is a option to tune it with a laptop if I were to purchase their new controller.
Pick the one you like or looks the best to you. I am going to be putting EFI on my Hemi Road Runner and am thinking hard about using the Holley system that looks like a carb, purely for the looks.
No matter what system you choose, it will be the fuel system that will challenge you the most and is really the hardest to get your head around. The EFI systems are easy really, but the fuel system can be a pain the first time you have to deal with it. Its not that it is really hard, it is that it is a fair amount of work and there is lots to confuse you with online. Don't believe the BS, you need a return line, so this means 2 lines running the length of the car and the tank will have to accept this and there are several ways to do that. Am in-tank pump is the best option however you can absolutely run an external pump. You will need 2 filters, pre and post (depending on how you configure the system), you will probably need a by-pass regulator as well (again depending on the system). You will need to install a O2 sensor into the exhaust as well as installing a temperature sending unit.
Last but not least, you will have to have a good electrical system and depending on what you have in the car may need a new alternator along with new wiring for it. EFI not likes but demands good clean constant power and this is the #1 problem people have with them, or better said the #1 cause of issues with EFI.