Frog Blast the Vent Core!
The scale of the capital ships, and the way their 'corpses' stayed around exploding was nice.
This is something that actually most people complained about, myself included. I wouldn't mind a burnt out hulk a la WC3/4 (even though they only hung around for a few seconds), but seeing the capship just sit there and explode drove me up the wall. Especially because the "damaged"/"destroyed" capship didn't look that different from the ship normally.
That's probably my biggest pet peeve about Prophecy, otherwise I also find it very enjoyable.