(I meant to type that I *don't* approve of Weir's decisions regarding torture & live subject experimentation but that it doesn't diminish my love for the character in the least.) So yes, her imperfections make her an intriguing and powerful character.

RDA was mentioning how SGU was simply not compatible with the rest of the franchise

That statement carries a lot of cred, given that RDA built the Stargate franchise from the get-go and nurtured it from its uncertain early seasons. I guess BW & Co. got cocky the more successful the franchise became.