The main problem with paladin alignment, aside from the possibility of the character builder screwing with you, is that they might BALANCE the class around alignment. That just doesn't work out well in the long run, since people will be constantly playing them against their required alignment, and either losing access to the character and getting upset, or being more powerful than they should be.
If they also build alignment into the class features, that also shuts down the class for non-alignment players. No class should be built around alignment, but you can certainly be comfortable placing alignment-oriented alternative class options in the Big Book of Alignment.