Yeah, I mentioned it briefly before, but even the most heinous example (in my mind), the Solitary Hunting variant, doesn't seem that broken if someone dipped and "stole" it. You still only have a single favored enemy at +2 (or +3, with certain racial foes and racial sub. level). It's not going to make much of a difference in most games, it's probably ok to just let it go. The bigger issue to me isn't the mechanical aspect, it's the "principle of the matter." I just don't like that level of powergaming, exploiting badly designed rules like that.
As for the something for nothing (and vice-versa) thing in general, I can understand a need for it. Not all trades will be nearly equal, and it makes sense that some things should could earlier or later than what they're replacing because they're that much better/worse. Say (just as an arbitrary example) you gave the ranger Wildshape as a druid in return for 4+ int skill points and loss of hide in plain sight. Wildshape is MUCH better than the lost class feature, but gaining it as a druid means getting it much earlier. Arguably, the skill point loss is making the trade overall "equal" (and I definitely would still call the ranger weaker than a druid) and is being paid for all along...is it fair to gain the class feature at 5? I don't mind such kinds of swaps in individual games for a specfic character that I approve of...I'm just not sure it's a good idea to publish them as "official" variants for anyone to use...
I'm just rambling now, don't even know if I actually made a point in the end.