Been doing some brainstorming and testing with a friend. Here's some ideas for Franky--slight variations on the broad theme, with detailed strategies:
Captains: Buggy, Vista, or Towel Nami.
Crew: BP Chopper, Hawkins, CB Helmeppo, Mr. 3.
Subs: Krieg or Broggy instead of Hawkins, Broggy or Tsuru instead of BP Chopper.
Stall Points:
Battle 3: Attack the turtle with Mr. 3 only, stall as long as possible. If additional turns are required, let a single marine take an additional attack.
Battle 4: Let the penguin attack to stall 1 turn
Battle 8: Use Mr. 3 to stall as long as possible on both the crab and the turtle.
All specials should be 3 turns or less away from readiness before leaving Battle 9.
Boss:
Turn 1: Attack.
Turn 2: CB Helmeppo. Attack.
Turn 3: BP Chopper. Eat RCV orbs, 2500-3000 HP regained. Hold any INT orbs.
Turn 4: Mr. 3, Hawkins. Attack.
Turn 5: Attack.
Turn 6: Hold INT orbs.
Turn 7: Kill (hopefully).
I just tested this with Double Vista. I got some really crappy orbs, but I won on Turn 7. With a few matching orbs, I would have had it on Turn 5. Keep in mind, this is with a MAX Merry--anything less than that, and you're going to have a bad time. I expect Vista + Towel Nami will be much easier, as the Double Vista HP buff is pointless once Franky negates it.
The reason for the staggered specials is primarily because Franky buffs defense on the second turn regardless of his AT, so using Mr. 3 at the start is really a waste. However, his Captain Silence only fires alongside his attack, so by delaying on Turn 4, you should get two turns of full-damage attacks against Franky's base defense, or half his defense if combined with Hawkins. CB Helmeppo is used on Turn 2 to negate the defense buff, and the heal is best on Turn 3, when you won't be doing any damage anyway.
Here's an example with the substitutions:
Boss, with subs: Krieg for Hawkins, Tsuru for BP Chopper:
Turn 1: Tsuru (Option 1), Attack.
Turn 2: Tsuru (Option 2), CB Helmeppo. Attack.
Turn 3: Tsuru (Option 3), Hold INT orbs.
Turn 4: Mr. 2. Attack.
Turn 5: Attack.
Turn 6: Hold INT orbs.
Turn 7: Kill.
Tsuru is a decent sub for BP Chopper (I'm going to be switching to her, actually), but requires tactical choices to be made depending on your crew. On Turn 1, the orb reshuffle often provides an improved first round of damage. This is usually the best choice. Turn 2, however, is the biggest damage round, and if the orbs are bad, Tsuru can turn things around into a quick kill, especially when combined with Towel Nami and Buggy captains. If using Vista, your HP will be reduced to its natural maximum on Turn 3, before Franky attacks. Here, Tsuru's heal is at its most effective, but can be detrimental if you're going to be reshuffling a bunch of matching INT orbs.
I find the choice to be situational, but with strong units, all three options should prove effective.
If Kiwi and Mozu show up, Tsuru will probably be more useful than meat generators, since you don't have to sacrifice Perfect hits in the pursuit of survival. I haven't encountered them on a boss fight yet. I imagine it's pretty rough.
Here's a non-Mr. 3 alternative from a friend of mine:
Captains: Buggy, with Vista or T. Nami friend captain.
Crew: Tsuru, X Drake, Krieg, CB Helmeppo
Subs: Any INT unit with big HP and damage for X Drake and Krieg, such as Croc
Stall Points: Same as above, except using Krieg instead of Mr. 3
Boss:
Turn 1: Tsuru (Option 1). Attack.
Turn 2: CB Helmeppo. Attack.
Turn 3: Tsuru (Option 2). Hold INT orbs.
Turn 4: Attack.
Turn 5: Hold INT orbs.
Turn 6: Kill
This one relies on the beefiness of Krieg and X Drake, to provide naturally high HP and attack. The higher their level, the smoother the sailing. Tsuru Option 1 seemed to be the safest bet even when running with a Vista friend. The potentially strong first round usually leads to a finish in Turn 2 or Turn 4, if all Perfects are landed. It also leverages a Buggy captain a bit more, giving him one extra chance at RCV orb conversion.
