It is one of the best spells for its level for sheer power, even if it has very narrow use.
I do think any form of conflicting control should result in opposed cha check, though. But as written, yeah, he can pluck off your minions one by one. You can of course just dispel the command undead, though. He can't dispel your cleric's Su ability to control them.
Command undead is only a problem if you throw around very powerful mindless undead, like a zombie dragon. For a 10th level cleric who specializes in this sort of thing, that's going to happen eventually, so this spell is a huge problem for you. Against your more run-of-the-mill skeletons and zombies, if a wizard wants to use his precious action to take control of one of them that's his perogative and less of an issue to you than another cleric.
My houserule on command undead is that anything with 5 or more HD gets a save even if it's mindless, and the spell is ineffective against targets with 10 or more HD.
Personally I have no problems with it. Less QQ and more Pew Pew as they say. It takes a 2nd level spell slot to take control of 1 of your undead. Just one. Then if you want to contest it you can just cast hold undead on any of your own undead he turns against you (mindless undead also receive no save vs this spell) and laugh at him. Animate dead is already an amazingly awesome spell that just keeps scaling and scaling with your levels (seriously, it just gets better and better and better). It's not hard to optimize either. Do you expect it to have no flaws or weaknesses?
You're still a 10th level cleric for goodness sakes. While the wizard or sorcerer is standing there trying to claim your legions of undead, you can be summoning planar superbeings to turn him into paste, or mushing enemies with your spiked mace, etc. About the only thing you need to worry about is some sort of mass-command undead, and if such a thing existed I'd recommend a wand of the same and some ranks in Use Magic Device. Or be a Mystic Theurge. They're the best necromancers anyway.
I ran a level 9 necromancer wizard who had also made a couple of simulacrae and had the leadership feat against a party of level 9 characters.
TPK. It wasn't even close.
Well firstly "halt undead" is sorc/wiz, not cleric. So no help there. In fact that only makes him more powerful in this regard.
I'm not expecting animate dead to have no weaknesses, I just think it is silly that a wizard can basically take control of an army I have specifically specced into building and payed for with nothing more then a second and third level spell. This is on top of the nightmare of having him flying and invisible and possibly simply dominating me as well. I don't think calling into question the power of these spells in this particular regard is unreasonable. An opposing charisma check against currently controlled undead would allow the spell to remain potent enough.
Yep. A spell that is anti-one single type of creature is pretty darn good at dealing with the weakest examples of those creatures. Imagine that. Wait 'till you see hide from undead. It makes invisibility look laughable in how potent it is. You're a 10th level necromancer cleric. This isn't a matter of being an unbalanced spell. It's a matter of overreaction. :P
Yep. A spell that is anti-one single type of creature is pretty darn good at dealing with the weakest examples of those creatures. Imagine that.
The spell doesn't distinguish between strong and weak, it just takes control. Taking control of a 4 HD zombie ogre with no save? That's perfectly fine. Taking control of a 6 HD zombie minotaur? Okay, but I think it should have a save. Taking control of an 11 HD zombie dragon? No, not with a 2nd level spell.
An 11 HD zombie is only CR 5. This is not a monster that a 3rd level wizard has any business taking control over, much less without a save. In a more sandbox-oriented game, 3rd level parties can encounter CR 5+ monsters, particularly if they seek them out.
Channeling - command undead:
"If an undead creature is under the control of another creature, you must make an opposed Charisma check whenever your orders conflict."
So you create an undead. Then you tell it - "fail this save". And then you channel - command undead. Now if a 3 level wizard comes along cast Command undead - the spell. He now controls the undead - but you get your opposed Charisma check...