I am specifically not doing weighting, because none of my previous attempts to tweak the RRV weighting were capable of overcoming RRV's majoritarian bias to a reasonable degree; with my test sets, every weighting I tried either gave the majority faction way too many seats, or way too few.
Re: 5. All else the same, you have the right of it. ...but why should that be peculiar? By our own ballots, I declared that I would receive greater utility than you, the seated candidate is closer to my ideals than to your own. As such, by the declaration encoded on your ballot, you would be less "harmed" by your ballot being used to elect an alternative than I would.
On the other hand, if our ballots were different beyond just our scores for that candidate, it might be your ballot that is apportioned to that seat. For example, if your ballot were 6/2/0 and mine were 7/4/6, then our relative contributions, our relative utilities, would be +6/+2/+0 and +3/+0/+2. After all, a ballot of 9/9/9 contributes no more to A being selected over B or C than a 0/0/0 ballot does.
So, no, I do not consider similar ballots being treated differently a flaw, because they are different. By my design, the more similar the ballots are, the less likely they will be treated differently, but because every reweighting attempt I've seen ends up less proportional than STV or SNTV (unless people bullet vote, neutralizing the benefits of cardinal ballots), there needs to be some cutoff at some point.
It sucks, no question, but I'm at a loss as to what other options there are for cardinal ballot PR systems under party list/slate of clones scenarios.