I was well above 70 for Agitha as I mentioned above. She's by far the hardest. For Lana'a L3 Gate I was around 80, but it was mostly because it took me a while to figure out that you NEED to take full advantage of the Gate's "double power" mechanic. Remember to use the EXP potion for your attempts so that even if you fail the mission, you'll get a lot of experience and be stronger for the next attempt.
I'm done with everyone but Agitha now. Lana and Zelda were both about level 70, Darunia was level 60, Link was level 90.
Great Fairy's problem wasn't damage received or dealt, just taken. Lana's Gate levels blow because getting enough kills was always a pain. Once I got the dragon riding thing to start working, she came along. Zelda's problem is that the Wind Waker is easily her crummiest weapon/I didn't realize that racking up 1000 KOs would be the best bet. For Darunia, grabbing the keeps and then building up kills was the way to go.
Great Fairy I had to use a constantly replenishing SP thing to make it go faster.
Agitha I'm honestly not having too much trouble with. The two tries I did I failed the first and cleared the second. The first I failed because those Manhandalas took down the base before I could get back. The second I a-ranked damage dealt and time spent, but I took 15000 damage so there was nothing for it. She's only level 45, though, so maybe building her up will beef her up?
For Agitha: Use the boomerang!
This video helped me a lot:
https://www.youtube.com/watch?v=sPX8Na5tGuc
For lv3 fairy I'd strongly suggest using the sp potion. It's the fastest way to clear mobs with her (even though her combos make you invincible, they're rather slow and you end up failing because of the time) and remember that her Y sacrifices defense (you will be taking 75% additional damage! be careful!) for additional offensive power. I got all weapons with characters lv65 at most.
The boomerang might help me cut down on damage taken, yeah. As to the Great Fairy, I tended to only use her Y to land the bomb-combo, which I found best for basically all situations not involving a moon.
I did all lv3 weapon missions before the 50s...
I think the lowest I've cleared one is Fi's, at below level 40 (like, 30-35?), but some of them I dunno. Part of the leveling up comes from the numerous failed runs trying to figure out how the heck I need to do the level to not lose the Allied Base.