For example, if I'm expecting the other side of the wormhole to be mined and under direct fire coverage, I want to send through cheap ships like fighters to soak up the initial salvos before sending my cruisers through to fire on the defenders. If they have 100 cruisers and a minefield and I have 20 fighters and 90 cruisers it could be the difference between victory and defeat, though most often it's just the difference between me losing 1500 worth of metal in fighters and 4000 or 5000 in metal+crystal in cruisers. Higher-end defense can make it more important; if I'm trying to flood an ion cannon or pull defenders away or occupy tractor beams I'd rather use T1 fighters than T3 or other more expensive ships.
So mostly it's cannon fodder tactics to save the non-cannon fodder a bit of grief. If for some reason the AI had a fairly homogenous defensive fleet in the immediate wormhole area I might want to send in the "takes very little damage from X or is very cheap" ships first, the "deals a lot of damage to X" ships second, and everything else third or even just wait until the AI fleet is down.
So another way of putting it is getting around the potentially lethal auto-targeting by not giving it any choices for the first salvo (if all it sees are bad targets, they'll still shoot at the bad targets). It's just a marginal gain, but that can be enough.