A lot of the things you mentioned seem to be more based on Crystal rather than original Gold and Silver.
I think Kris was the only aspect I mentioned that was Crystal exclusive. Everything else I brought up (barren Kanto, horrible level scaling, watered-down Team Rocket, etc.) were common issues in all three games, unless I'm forgetting something and Crystal actually fixed those things. It's been a long time since the internal battery went dead in our Crystal cart, though allegedly my brother still has it somewhere.
But yeah, I completely tossed Silver to the side once Crystal came out and never went back to it, except maybe to trade some exclusive mons over to my Crystal cart.
That and Giovanni was nowhere to be seen in gen 2 either. That one confuses me.
To be fair, I did offer this caveat:
But to answer the question, and honestly, a lot of these are holdover flaws from G/S/C:
Granted I think the whole Giovanni thing would be hard to correct without significantly changing the story of the games, but (at least for me) just because a problem was in the original game too doesn't mean I'm going to be more forgiving of it when it appears in the remake - it still negatively affects my gameplay experience, even if it "should have been expected because the originals had it." Just like all the water in Hoenn and its remakes. Speaking of which...
If HG/SS is mid and so is BD/SP then by default OR/AS and FR/LG are the superior remakes. Long live gen 3 the best generation.
I'd actually only say FR/LG since OR/AS were among those "later games that I skipped entirely" lol
I'd like to close this with another. and completely unrelated unpopular opinion:
Sword/Shield work better as trainer dress-up games than they do as actual Pokemon games.