@February:
Since Luffy hadn't seen any of the stuff Arlong had done to the island or heard any of Nami's backstory when they had their boss battle, it was essentially an ideological conflict over what a nakama is in the first place and how their dreams and tallents can be used/exploited. Arlong said a lot of the same phrases that Luffy uses about nakama, promises, ambitions, etc. but then perverted them with his actions. Since that opposition to everything that Luffy stands for is the core of his character, he couldn't join the crew without having changed his elemental motivations, ambitions, and perspective enough to be a completely different person. (Which is possible, he could have had a major revelation, but he wouldn't be the old Arlong any more)
HOWEVER
The new HQ is just slightly on the other side of the Red Line and Marine/WG characters can show up at any point in the story. They probably know exactly where the SH are going too. I am not satisfied that after all he has done for the SH crew, they are going to just treat personality-less Kuma as an enemy and try to kill him. I think he needs to be rescued. And isn't that how all the nakama tend to join?
He's not a "boss" in the sense that he commands a group/army but he is definitely at the boss level of strength, and his appearances have been in boss-battle-like locations in the storyline.
How he will fit on the ship is another issue…
like I said, a "partner" is not different from a "Nakama/crewmember"
Let's take a look at other "Boss villain turned Partner" characters.
I'd say they're called BOSS simply because they had a 1 on 1 with the main character of the story (luffy)
Smoker -> Croc's Casino
Clown Buggy. -> Impel Down, Marineford
Crocodile -> Impel Down
Hancock -> Since she became obsessed
Kuma -> Since he restrained himself on Thriller Bark
now for mini-boss characters
Hachi -> even fed them takoyaki
Perona -> Helped Zoro
Mr. 3 -> Impel Down
Mr. 2 -> since arabasta
Duval? -> who cares?
Anyway, i think you know what i mean. Im not referring to the former Boss=Partner thing to be the next Straw Hat. That is highly unlikely. Unless Jimbei bitchslapped Arlong for being a bad boy and changed his ways.