I'll just chime in and agree that it's a stupid ruling. I believe it was done when they changed how they looked at all the creatures in the MM. They put all the creatures into "classes" of a certain type. It used to be that you did have to choose vampires over liches, versus skeletons or zombies when choosing an Favored Enemy. And it makes sense for the most part. Again, though the argument for that rule falls apart most readily when you agglomerate a varied wild bunch of creatures into a class and then choose FE by classes instead of individual species.
Rangers, in their heyday (which, IMO was AD&D 2.0) skillswise relative to other classes, chose their favored enemies by a single race/species. Now it's an entire class of creatures. For a class of character, this actually makes the selection a bit more powerful when it comes to slicing and dicing, but as a logical rule, it falls pretty flat.
The idea, though about orcs, vs, goblins, vs kobolds, say, as humanoids also isn't sound as an argument, because it is not just the anatomical differences (which are slight) it's their way of culture, their way of fighting, how to inflict the most damage is not necessarily only physical damage. Knowing what frightens them, what emboldens them, what makes them so angry they forget tactics or strategy, or what panics them all are taken into account. Of course, there are anatomical differences too that might make a difference, but it isn't just that.
I agree that the way FE is selected now isn't as 'good' as it once was, but as pain said, 'dem's da rules.' In my module design (on paper for PnP) I don't even worry about that, because via Rule 0, I can do pretty much whatever I wish and damn the rules, full speed ahead. And so I do some things very differently. Here in NWN2-Land, I follow the rules the devs put into place and accept any decent changes to them via scripting that others have instituted.
It's an adjustment, though not one too shocking or hard to deal with for me. I suggest you manage in the same fashion. It's better for your digestion.
dunniteowl