For me it has to be the second to last mission in the Episode 2 Confederacy campaign. When you land your troops on the asteroid and the AI just tries to swarm you.

For me, I find that the two campaigns for the Episode II (so Confederation and Republic) are pretty repetitive.

For the hardest one, I would say the Gungans, since I still have not been able to finish the last mission in medium mode.

I haven't played the whole game yet, but so far it's been the second to last mission on the Gungans, its taking me forever to beat.

with enough patience you can clear the entire map just with the starting fighters and air cruisers...

One of the Episode 2 Confederacy missions, the one where you have to destroy the Gal Rep spaceport for Boorka the Hutt. Over 6 hours of game time and every attack I make is butter at a hot frying pan.

Going to look for cheats for it, I'm fed up of it.