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Originally posted by Gandalf Parker:
Id have to question a couple of those answers.

There are commanders which SEEM to have some benefits to handling certain troops. Abyssia with the dragon handlers, Ctis with the lizard handler. Doesnt Pythium have one for hydras? Not sure the names for all of them but I could look them up. The way they read I suspected they help avoid routing though Ive never actually tested it.

Also, combining 2 and 3, I often give standard commanders things like a dragon helm or a bow to give them something to do while "stay behind troops".

The other answers I agree with.

Well, when playing Pythium and Abysia I usually don't bother with the special commanders, I just give the beasts to standard commanders and didn't see any difference. Maybe I've missed stg as you suggest (the special cmdr giving morale boost or stg) ?
And the question was formulated for "normal" cmdr (hoplite, Ulm leaders, etc) where it's certain that there's no special effect associated to the fact that one is named "Hoplite", the other "Hypaspist", etc..