I have been running both systems for a few years now and they both have their pros and cons
On my GN, which is a drag-drive car, the dominator is the best choice IMO. With all the crazy stuff I do with that car, the flexibility it has and the ease of use of the software with endless input/outputs that are easily configurable and the advanced tables make it the best choice. Especially for a DnD car.
My Ttype has the ECUGN which is easy to install has plenty of options and IMO does flex fuel much better than the Holley. That ECU is really nice for the Buick guy who wants to plug one into a mostly stock TB and have WBO2 control with flex fuel which is totally PnP. IMO It is also worth the extra $$$ over the MS3 PnP with the added feature Eric and Bob built into the system.
Boost control is a BIG win for the Holley, I don't use the Holley traction control and have a Davis box on the GN that I haven't used much......yet!!
MS3 software IMO sucks, but the wiki and online info is pretty extensive making it easy to get help plus Eric and Bob are awesome and always respond to questions and are real assets to the Buick community. I have my Ttype apart right now for some updates and I am getting ready to dive deep into the ECUGN setup again. I will be adding CO2 boost control with dome pressure and a bunch of additional inputs/outputs. I am also building a custom harness for it mostly because I hate the factory harness that much. I am actually separating the chassis harness and ECU harness completely and making them two independant harnesses if that makes sense. It will also allow me to swap ECUs easily if I ever decide to put a Holley or even Fuel Tech in it and I am making the ignition pinouts so I can run different systems if I decide. Right now I am swapping to truck coils with wastespark. I will also drop from 11 different relays under the hood to just 4 or 5.
I have not had any issues with the WBO2 on my Dominator. I also have a spare just in case which if you have a DnD car you need a spare of everything anyway. NTK sensors have never been cheap but if you run any type of leaded fuel you will need one IMO. All systems seem to use the same NGK PN 24300 L1H1 NTK sensor. The different manufactures change the plug and add a "calibration resistor" to make you buy thier sensor. FAST, Accel and now Holley all do this. IMO if you are not going to run a leaded fuel I dont think there are any real downsides to running a Bosch over the NTK.
Glenn at MAD Racing sells the NTK sensors with calibration resistors for the different systems for not much more than they cost new. The NTK sensors even when buying from a parts store have always been expensive even since the early 2000's when we first started running them. When Holley has a sale you can get them for $280 which really isn't that bad.
Cons for Holley, customer service is HORRIBLE and Holley is NOT cheap either. The cost vs service you get IMO would make me use a Fuel Tech or Haltech if starting over again knowing what I know now. I would avoid a Term X all together I have seen issues with them. We also had a brand new HP lock up on the dyno, sent it to Holley they admitted it was an internal issue and ECU was junk. Since it was purchased over 90 days ago they told us to have a nice day and sent our paper wieght back. Assholes is about the best I can say about them and I have even more BS stories in trying to deal with them they really suck.
I have played around with both the the Haltech and Fuel Tech systems and they are nice with plenty of cool features and options but I do still feel the Dominator is a better system overall. You can't beat the software, the configurable I/O's and the endless capabilities the advanced tables that can be designed to do just about anything you can think of with the use of the configurable I/O's which really makes that system far beyond the others.
I am probably going to use a Fuel Tech on my next build which is my 67GS twin turbo pro-touring car I am hoping to tackle this winter. It has a few features I like for that build. Like the built in gyroscope and accelerometer and display screen. Plus I like how it is modular and the price is a little better than Holley too and dont get me started on Holley custmer service lol. IMO Fuel Tech is a really good system for a car that is more track based adn the end user that wants something simple and easy to install and use with good support. The Dominator does a lot but it is also easy to get lost in all that it is actually capable of. Most people I see with a Dominator really dont even need one and usually are not using it for what it is fully capable of doing. If I were doing a build and considering an Holley HP or Term X I would definitely look at Fuel Tech first. If I was doing a LS swap I dont think there is anything better or cheaper than the Haltech Rebel.
In closing I dont think the new systems are really that much better than the old systems like Accel DFI or FAST XFI in terms of making more power or being any better at running the engine. They all do the same thing when tuned correctly by managing air spark and fuel.
FYI I still have not gone as fast in the quarter with my GN today with all its modern widgets and do dads as I did in 2009 with the Gen 7 and a distributor!!! lol!!