Basically they are eliminating many enhancements, while requiring us to take "filler" enhancements to get to the ones we use to get with no prerequisites.
PrE's used to have 4 or 6 AP's worth of "fluff" filler prereqs like "Improved Heal Skill II" for Radiant Servant. Now it has 20 or 30 AP's of filler prereqs... And if that's not bad enough, the mediocre enhancements like say Dwarven Axe Damage II (equivalent) now have as much prereqs as PrE's used to...
There really is no actual reason why they need to break builds, unless they are doing it on purpose.
I guarantee you that Squeek and Varg know that just eliminating the "points spent in tree" requirements and making all the old enhancements available in tweaked or rebalanced versions where needed would allow 100% of current builds to be replicated in the new system. If they have to throw out one ability or another due to balance issues so be it, but there's no intrinsic reason they NEED to break builds... the tree system can absorb the old enhancements and use "points spent overall" and then NO ONE gets a truly broken build.