I went with an aftermarket ECU on my project, and recently switched back to a factory ECU. With the right tuning, a factory ECU is hard to beat for overall drivability and performance. And factory ECUs have factory knock sensing built in - which is a major bonus in my view. Those cast pistons in the LS motors have very low tolerance for detonation. And if it's tuned MAF-only (like the GM crate ECUs do) it will be very tolerant of different performance modifications.
But the aftermarket stuff is very functional as well - hard to go badly wrong if you stick to the major names mentioned above.
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