The command squad is definitely a better fit for Black Templar Commanders/Chaplains for really one reason: They can gear up to be CC beasts! While this squad is still going to be more expensive than a normal squad, it is (usually) cheaper than its terminator equivalent. Now, obviously this squad isn't as survivable as a terminator command squad. However, it makes up for that with customizability. You can tool this squad up to take on just about anything and have a good chance of coming out on top in any fight.
Cons: Not as survivable as terminators, and can't take as heavy weaponry for shooting.
Pros: Can take an apothecary, which helps with the survivability, and is customizable to take on lots of things.
Some of the things that make this squad unique is its ability to take terminator honours, and the ability to take veteran skills. That's right, this squad can be tooled out exactly the same as its C:SM counterpart, but with Furious Charge, Infiltrate, or Counter-attack. (Personally, I'm looking at Furious Charge for these Power Weapon armed killers).
Now, with the Command Squad, there are obviously many, many possible builds that are effective for different armies. I will be listing my personal favorite, and one that can be used to surprise many an opponent. (I'm including the veteran skill points cost for a leader in the points cost as well)
CC Command Squad: 5 Marines, Apothecary, Fighting Company Champion, Sergeant w/ Terminator Honours and Power Sword/Storm Shield, x2 Meltaguns, Furious Charge - 193
This squad may be best assaulting out of a Land Raider Crusader, but it is pretty good no matter how you run it. It is also pretty straight forward in use. Meltagun something (like that Chimera) then charge what comes out. the storm shield on the sergeant is for those stray low AP shots, and for those Power Weapon hits. And of course, it has Feel No Pain!
"Sneaky" Command Squad: Apothecary, Fighting Company Champion, Sergeant with Terminator Honors and Power Weapon/Combi-Melta, x2 Meltaguns, Infiltrate - 188
This command squad is for using the Infiltration to act as a deterent for your opponent to just leave his tanks sitting in their deployment zone. Scare the enemy towards you tactics. This squad requires more finese to use, but if you know anything about the Space Wolves, use them like SW Scouts that can CC stuff.