Do like I do 

Since they're new I want to show them comp stomp, but after they're accustomed to the races they like, move onto humans.

If they're competitive you'd assume they would want to defeat a human. Those games are 25-40mins.. Sometimes a little longer, but once one team has a decisive victory somewhere, most opposing teams will yield rather than dragging for another 45mins.

Your average 5-v-5 PvP game only lasts about 1.5 to 2 hours.

Well I managed to get them to taste it, one as a TEC Loyalist, the other as the Rebel.

I had currently been running flagship victory to prevent absurdly long games, however I'm beginning to think that's a bad habit. A second free cap at start feels a bit like cheating to me, yet endgame it doesn't last nearly long enough.

I will test Diplomacy/Research victories to see how those behave. Also while I stated they are competitive, I offered them online human battles and they both decided they wanted ez-mode learning with training wheels first. I wanted them to get used to the keybinds, map movement, map awareness, and most importantly research / planet development.

Once they get the hang of it I'll start making them fight people.

While the 1.5 patch will fix most of these, in my experience it usually doesn't work out that way. Abilities like ion bolt and phase out hull means a good ambush can kill a player who isn't paying attention to his flagship easily by keeping them from jumping. I would have to say my favorite game on ICO ever was a 4v4 flagship game.