Agreed. I wouldn't want Skrulls being used to ret-con established storylines and character fates.
However, clever use of Skrulls with existing/new characters can be intriguing...
As an aside, Agents of Shield trod a delicate and sometimes shaky line between trying to be connected with what was happening in the MCU and forging its own identity. Once it went its own way, it had a mildly interesting mythology that was often a bit too confusing for its own good. I stayed...