Dragons are a nice challenge, though if there are lots of them you're in trouble. Shooting up cruisers with Tempests while dodging flak and AAA is fun as well (works best with an Aeolus)
One thing I really didn't like was the penultimate mission of FS1, where you launch from the Bastion to chase down the Lucifer. A HoL destroyer jumps in across your path, and launches a load of Thoths with Flails that push you miles back the way you came before you can kill 'em all. Irritating in the extreme. Getting bounced around between several AAA beams without being able to escape is a pain. And the tail AAA on a Lilith cruiser is possibly the most annoying thing ever, especially when trying to kill it with a fighter.