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LS2 uses the E38 and L76 uses the E40.

The currently available software for both of these models is fairly weak compared to the LS1 stuff (the software comes from the same manufacturer though).
Firstly, the transmission tables for the new models are virtually useless, it really limits trans settings, (such as setting the auto up for the drags).
In general, there is just less adjustability in all facets of the program. All of the basics are there but it's the "smaller", less commonly used tables that I miss. Some of these smaller tables never get touched by tuners, but I like to adjust them slightly to improve drivability. DFCO and Lean Cruise are two that instantly spring to mind. DFCO (Decelleration Fuel Cut-Off) can be modified to enhance engine braking (as I did for Leeroy and Aussie Mike), and Lean Cruise (when properly set-up) can obtain great fuel economy.

To be honest most of you, perhaps 95%, will be perfectly happy and probably not even notice any of the differences.
I certainly can't do without access to ALL trans settings because I need to optimise the auto for the drags AND cruising. If I was running a manual I probably wouldn't be so concerned, but I would still miss the "nice touches" that the LS1 software provides.