I look at the prospect list as propaganda in OOTP and in real life. Same as I look at preseason predictions, again in both OOTP and real life.
As far as v25 and the expanded ratings scale? I have found my minor leagues make a lot more sense than they did in previous versions. In previous versions I would assign players to minor league clubs almost as a "best guess" after looking at ratings and stats. In v25 I would say I know why each player, be it filler or prospect, is where they are. I do still, as I always have, use the OV/Pot as a tool that draws my eye (but not the only tool, as IRL one needs to look deeper), while using each players actual skills along with stats to make decisions.
Does every rating work when plugged into the top prospect list? No, but I don't really care and, it never did in v24 or before either in my experience. A top prospect list is like preseason predictions, a best guess, that many times ends up meaning nothing when those top prospects try to make the jump to MLB.
That's my take, others milage will of course vary.