The flaws in the storyline are way more than just minor. They are complete changes to the Superman story. However, they don't spoil my viewing pleasure of the series, as I don't mind them. And they are what make Smallville work so well.
I think talking about the hated things about the series as a whole is on topic, as it applies to the many things wrong with particular episodes. Like, when you mentioned Lois being introduced. That's an episode. Simularly, as with Lois being introduced early, the whole thing with Lex Luthor and Clark being buddies for the entire 4 seasons (on more than off) is just a complete joke in terms of consistency with the Superman timeline and legacy(?).