You pretty much hit the nail on the head for my reasoning - I don't really feel the need to give my PC wizards a "personal, loyal, flying artillery platform" as part of their free class feature, and that, along with the vaguely worded text is the justification that I used when I made the ruling. My PC just nodded and picked a viper familiar, and that was that as far as my group went.
I understand the logic behind allowing the trick to work (and I'll have to remember to ask about it next time I get a chance to play my conjurer - he has skill ranks to spare, a bunch of wands, and soon an imp familiar). But there is still an in-game case to be made against allowing familiars to use every skill that the master possesses. If Endarire's DM doesn't want to allow the wand-slinging bird, there's precedence, and he wouldn't be the first DM to make that call.
For what it's worth, I don't think WoTC thought through the ramifications of familiars sharing ranks with their master - it almost certainly wasn't RAI to have the familiar count as a free +2 aid another on every skill on top of everything else.