As I understand it ...
I think if you build E-LSA, even though you might add lights and IFR instrumentation, you can't fly IFR or at night.
On the other hand, I think if you build E-AB and include that equipment, your program letter will allow for both. On the day you don't want to visit the sawbones any longer, you just stop flying IFR & night, and that's pretty much all you have to do. (Just limit yourself to sport pilot operations in an aircraft that meets the prescribed requirements.)
The Repairman / Inspection privileges are different. I think it works so that in E-LSA, you can sell the airplane and the new owner can get a certificate. With E-AB, there will only be one certificate ever issued - the successor owner would have to hire a A&P for just the condition inspection (but not for maintenance).
The consensus seems to be that once the E-LSA airworthiness certificate is issued, you can change anything but that it has to conform to the S-LSA prototype at the time of inspection. I'm pretty sure the operating limitations will specify when to notify the FSDO relative to changes. Just my opinion - if you're thinking of changes that entail Engine, Wing, Fuel tanks and / or Landing Gear, when you run the numbers, you might see it more advantageous to just build it E-AB to begin with. As to the conceptual value difference of E-LSA vs. E-AB, it ought to be somewhere near the present value of about 5 condition inspections, this number being reduced by the value of additional utility (such as night, IFR, etc.). Seems like it would work out to be pretty close.
YMMV - me, I'm waiting for Katie B. to update on the Jab 2200 FWF kit and what plans there might be for a Jab 3300 FWF kit.