That's... a hard one for me to answer.
I more or less tackled the missions from left-to-right on the map on the GCN version. Now I'm tackling the missions in story order.
I don't know which one for me was the hardest
, per say, but I can say the following were a BITCH to A-Rank:
Radical Highway - Missions 1, 4, and 5 - for some reason, I often was about 1000-2000 points short.
Route 101 and 280 - Every friggin' mission, ESPECIALLY Mission 4. You know, the one that makes you restart if you barely scrape any wall.
Knuckles' and Rouge's Mission 4's - Especially on the ARK. Don't like the random aspect with a time limit. I found Hard Mode to be the easier mission since the objects you search for are always in the same place.
Tails' and Eggman's Mission 4's - Well, they were until I got used to the slower movement.
I'd say that's about it, A-Rank wise.