It isn't the 17/2/1 builds that we're worried about. It's the 12/6/2 and 13/6/1 builds.
Previously you'd have a smattering of enhancements from the 6 level class, enough that you could get the PrE. The rest would be from the 12 or 13 level class. But with the 3 trees only, you'll (probably) be losing access to enhancements that you had right now, effectively creating less build options.
Take the commonly used Rogue as an example.
Haste Boost is likely to be in Acrobat.
Sneak Attack and Subtle Backstabber are likely to be in Assassin.
Skill Boost, DD and Wrack Construct are likely to be in Mechanic.
These are enhancements that the majority of Rogues currently take. That's all three trees, so which of them do you want to give up to get your PrE from the other class?
Which other one do you want to give up to possibly get a racial PrE?
Multiclass characters will surely be impacted under the proposed system. How much they will be affected will vary on a case by case basis.
That was the entire reason for
this post and the conversation that followed. While the suggestion in that post would still be restrictive to a certain degree, it would be MUCH less restrictive than the current proposal.