I agree that it might only make a small difference. I do think that it is quite an important change that might make it difficult for youngsters.
There are probably more significant reasons for this, which were discussed in this thread.
However, The transition period effect (points from the end of 2008 were much bigger than points from 2009) might be another reason (it affected seeding of course).
Frankly speaking, following the rankings week after week, looking at the players" results quite closely, I don't think it changed anything, simply because :
- in 2009, there were very few emerging young players, coming even near to top-100 : only De Bakker (88), and then you have to go to IStomin (generation 86) and then you have generations. Some players who stayed in the top-100 because of their results in the end of 2008 were also quite young, like Golubev or Mannarino. In older generation, nothing to note in generation 85 (the ones who didn't reach top-100 stayed quite far), and in older generations, players had ups and downs but not really players "emerging in top-100" that year.
- the players who succeeded in challengers last year were pretty old, even older than on the main tour, except Dolgopolov but anyway he mostly succeeded on clay and he wouldn't have got any main draw entry thanks to that.
Previous year it would have been quite different with a little bit more young emerging players, but last year the old players really had even more power than previous years. Actually inside the top-100, many of the players who improved their ranking a lot (and then were damaged by new system) were old players : Haas, Hewitt, Ljubicic, Ferrero for instance.
Anyway what's clear is that challengers have not been a place for young players' successes recently, rather for old ones, many born before 1980, see Luczak for instance
This year it's better by the way : especially many players born in 1987 emerge this year (I know they're 22-23, it's not considered young by some, but nowadays many players emerge around 22, I mean not the very-top ones but the ones applying for regular top-100) + Dolgopolov and De Bakker for generation 88.