I personally am OK with bonuses as long as they are coupled with "real" bonuses, resulting in a balance lever for the initial passive.
Cait has Headshot as her main passive and to balance that Riot lowered her Base Attack Speed and gave her that bonus so that she doesn't Attack as fast as any Crit Carry in the Late Game while maintaining a balanced Early Game.
Yasuo has the Double-Crit, which speeds up his powerspike while trading his Late Game DPS of a Crit Carry. While he is overloaded, his Passive Shield covers the "boring" bonus from his Passive.
Pyke has the Grey bar, which would be broken if he went Tanky, so making him always squishy would lead to a higher risk/higher reward champ by offering him Damage over HP.
Shyvana's and Karma's in my opinion should be moved to their ultimates and replaced with almost anything. They simply don't feel rewarding or unique in any way, at least compared to the bonuses above.
I don't think Passives have to be core parts of champions, but they should at least feel like they have somewhat of an individual impact from a kit or at least enchant it. If it lacks both, then it is kinda doomed from the start to be insignificant.