You should probably talk to your local tunning guru to see which system he prefers. I'm sure you have the ability to learn the software, but you probably shouldn't try starting from scratch with a turbo engine.
You haven't mentioned cost yet. Using a GM computer and harness can cost as little as $150 if you buy used and modify the harness yourself. Get someone to help you with HP Tuners and your up and running with relatively little investment. If you have the money then Holley's EFI is a great selection.
In my case I already had experience with HP Tuners so I chose the stock ECM/harness. Since getting my car up and running with the turbos I've added an MSD 2-step and a Boost Leash controller. I'm not sure how much money I've saved anymore by using the stock ECM vs a Holley Dominator EFI. Try to take in the whole picture of cost, features, future expansion, and ease of use when you select which system is right for you.