Well a good escort mission IMO is something with plot, storyline and different parts to the mission. So it starts off normally, but then, maybe a cruiser jumps in 4,000 clicks out and the player is sent to intercept it. Then enemy bombers come and try to destroy the convoy ships while the player is away. When the player gets back, another interesting thing happens, like enemy transports jump in. This way you can maintain the "oooh, this is a new type of challenge" atmosphere for longer than 10 minutes.
"Into the Maelstrom" was good because it wasn't just loads and loads of Hercules wings jumping in one after another (Surrender Belisaurius was okay because it was relatively short, and it had an interesting bit at the end). Into the Maelstrom wasn't only an escort mission, you needed tactics to destroy the Maelstrom's beam cannon as well as stop the Medusae from killing off your ships.
Additonally, PI's first mission was good because we could see a lot of new stuff, despite it being uneventful in comparison to the other missions of the campaign. Like the Aten actually doing something, and the Vulcan primaries.