Some observations:
The LSx-compatible Holley kits are the HP and Dominator kits, which are not of the "self-tuning" variety. This is, IMO, probably a good thing. The only self-tuning kits we've used - the FAST EZ-EFI - have yielded lousy results for us, other observations on this forum notwithstanding.
Both the Holley and Factory ECUs support knock sensing/retard, which I consider almost a must-have when tuning LSx motors for max performance - they have such efficient combustion that even a few degrees too much spark can push you well into knock and destroy an engine fairly quickly.
Factory ECU uses a MAF, which is an extra consideration when designing air intake. Factory ECU requires either HP Tuners or EFI Live software/interface to tune, which is quite expensive to acquire if you want to do your own tuning. Also, Factory ECU tuning is significantly more complicated in some areas than the aftermarket systems. But they are pretty much "plug and play" to get up and going.
The Holley systems offer more configuration flexibility, and more control inputs and advanced options as noted above, but there is a little more initial setup required as a result. They use wide band closed loop instead of MAF to control WOT fueling, a more expensive but more precise strategy. The tuning software and parameters are simpler to learn and use.
It seems like either of these can work just fine for your application, but either absolutely must be tuned in order to work well with your custom application. So the choice might come down to which system you feel more comfortable getting installed and tuned, either by you or by your chosen expert.
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