I didn't really want to get into comparisons of this sort again, but I feel I must to respond to your points. I'll try to be brief
When I mentioned a few posts earlier about 7 wildcards (Schwantz) vs 4 wildcards (Spies), they weren't numbers pulled out of a hat. The difference of 3 hardly equates to "2 years", and had Spies taken the ride right in front of him at Assen in 2008, it would have been only 2 less wildcards. Given the difference between support levels for those wildcards, 2 strokes vs 4 strokes, the fact that Spies spent a whole year in Europe in 2009 winning a championship, I don't think there's a whole lot of difference between 1986-1987 and 2008-2009 as to what experiences each rider had behind them going into their rookie seasons (or at least not enough to use as a major point in an argument!). And who knows what kind of tyre issues Schwantz had to deal with in that period?
To put it another way, 1986-1988 Schwantz had 22 GP starts; 2008-2010 Spies will have had... 22 GP starts!
A better comparison for Spies 2010 season are the rookie seasons of Lorenzo and Dovizioso from 2008, at least in terms of points. Spies needs to only 9 points to go past Dovi, which seems likely, but needs 28 to get past Lorenzo's mark (which would require at least a 3rd and a 4th place). The pluses and minuses here are more easily quantifiable: Spies has a lot more experience with bigger bikes and 4 strokes vs the years the other two spent in the GP paddock (and all that entails); a higher degree of difficulty I'd say for Spies, and Lorenzo having ridden a full factory-supported bike is again in Spies' favour--although Dovi's 2008 satellite Honda would be a plus for him against Spies. If I had to rank the three, I'd put Lorenzo first (he was under a lot more pressure in 2008 than Spies this year), Spies second and Dovi third; but all three have had excellent rookie seasons. Will Spies kick on like Lorenzo, or 'stagnate' like Dovizioso?
For the championship I agree with you, whole-heartedly, because points are the system we use to determine the winner. P2 and P3 have their lesser prestige, too, and there are always contract considerations. But beyond that--for rookies/riders not in the thick of the championship hunt--I'm not so sure. As an extreme example, what would Rizla Suzuki prefer: Capirossi has an abyssmal 43 points this season, with a best place finish of 7th. His season has been ruined by injury, reliability problems and a bike that's a heap o' ...... He should limp home at Valencia to around 50 points. What if they could've got 50 points with 2 wins? 2 wins and a string of crashes/bike failures/injuries probably still looks a lot more palatable to the team and the sponsors than 0 wins, a string of crashes/bike failures/injuries/and poor finishes--and, perversely, would even show that there is more potential in the bike!
Schwantz's 1988 season is a less extreme example of this, I think. 2 wins, 2 more podiums, 1 fastest lap, a handful of solid top 5/top 10 finishes and some spectacular crashes. I'm sure the sponsors were happy, and the team, too (no doubt they'd've liked less crashes, but it's easier to teach a fast rider not to crash than it is to teach a slower rider to go fast; Revin' Kevin unfortunately being a bit of a slow learner in that department).
It did take him 6 years to win a championship; he was indeed a slow learner. 1989 could have been his year, with a bit better (and more reliable) bike and if not for too many first lap crashes. But in 1993 Rainey himself said that he knew it would be tough because he saw that Schwantz had finally wised up. As cruel fate would have it they both only crashed out once in that season Schwantz (and Barros) were taken out by Doohan at Donington, and Rainey's life changed forever at Misano. Wayne ended his career with 3 championships, and 24 wins; Kevin 1 championship and 25 wins.
That he may, the potential is certainly there. As Schwantz ever so bluntly put it, though, he needs to take it to the next level to do it. But at least Kevin did say at the end: "He'll do well."