I should have added "easily." I know that most, if not all, games will have the good guys winning against the bad guys, but that doesn't mean all bad guys are automatically a threat I care about. By having us completely destroy a whole legion of Kett before we even get a good glimpse of their leader they're already made out to be barely a threat. Even when looking at Saren as the big bad of ME1 which, yeah he is (it's been a while since I played it), he's still shown as a threat to the player character directly. Your point about Sovereign is a plot hole that one thinks off after the fact, it doesn't affect ME1's actual threat in Saren nor does it affect his big chilling speech near the end; it's such a minor point whereas the issues with the Kett are clear from before Mission 1.
Fixing the Kett is an incredibly easy fix; just have the big bad Kett Leader come in and shoot your dad before running off. The prologue felt like it tried way too many things; it should have done three things: 1) Introduced and made you care about your dad/his sacrifice and 2) Introduced and made you want to defeat the Kett whilst establishing them as a substantial threat OR introduced the Remnant Vaults. Everything else should be done later; Cora, Liam, the Remnant Vaults, none of them needed to have time dedicated to them in the first mission.