It brought the players joy and a feeling of accomplishment to choose powers, use them well, and win tough victories because of that choice.In the game, the PCs hear some rumours about undead. They re-spec their PCs in order to be effective against undead. They go and fight the undead. The fights are tough, but because they optimized vs. undead they are successful.
They pat each other on the back for their smart choices. They're happy.
The DM knows that the original encounters only featured a sprinkling of undead. When the players changed their PCs he altered the encounters. The choice to re-spec, which the players were feeling so good about making, was actually meaningless; the encounters would have been just as difficult no matter what they had done.
Its only meaningless if you view D&D as a sort of metagame duel between players and dungeon masters.
Which is a bad way to look at things, because that makes the entire game essentially meaningless, since the DM could win any time he wants to.