The clue is pretty obvious. IT'S SOMETHING THATS NOT LIKE LUFFY, AND ONLY HIS CREW WOULD KNOW ABOUT IT AND NO OTHERS (well, except those who understands him, like Rayleigh or Vivi. Or we as the readers supposedly know it, Heck, we've been with him for 10 years ffs)
So why dont we just break it down to see it easier.
1. Luffy, Jimbei, and Rayleigh show up and steal a marine's ship and do a sea burial ritual.
Would Luffy do this? The stealing, yes. But the ritual? we haven't seen Luffy dies this kind of thing, and I don't know if its a common tradition in OP verse or not, if not then its likely that some of his crew wont know the meaning of it. So I'll just take the circling ritual for what it is. A burial rite, no hidden message.
2. Luffy storming in the plaza alone, rang the bell 16 times, threw a bouquet, and bowed his head.
Storming in alone is a typical Luffy, the meaning of the bell itself is known only to the marines I think, so it doesn't make sense to use it to deliver a message (except if the number 16 is the message, which I doubt. But can anyone tell me what the number 1 and 6 in japanese are and if they mean anything? 1 is Ichi I think, and 6 is Roku. Ichi Roku???? I'm not good in jap so if anyone can correct me)
As for throwing the bouquet and bowing his head, honoring the dead is not unlike Luffy (we've seen him saying prayers to Bellemere's tomb, waaay back at the end of Arlong's arc).
Conclusion, during the whole ordeal, the only thing that I think is not like Luffy, is the fact that he returned to Marineford and did all those things. But he hidden message is something else, which why I'm banking it to be the tattoo.
Yes its weird that its not made that obvious, but then again, we haven't been shown the newspaper in its entirety so maybe its shown somewhere. And the theory about 3D2Y makes sense also. Rayleigh said to meet up in 3 days, it was crossed (according to the slight pic we see). 2 years to train and get stronger also makes sense. This is not Naruto, Bleach or DBZ where we get instant power up out of nowhere, and no room where 1 hour there equals x days on earth. Here, they train, and it takes time.
Anyway, thats what I think