CP9's fights were relatively boring (still good, when added to the backstory). Whiskey/Arabasta had a great range of powers. Water 7 did have more intense emotional peaks (Usopp vs Luffy, Franky's backstory, Going Merry). Water 7 was more mysterious (Franky, Iceberg stuff) and had more interesting characters. Water 7 had more characters I desperately wanted to see get fucked up (fucking Spandam, Lucci, Jabara) than Arabasta (just Crocodile). CP9 was more of a mindfuck (even though I liked the political twists of Arabasta) and was kinda spooky. Hiluluk and Tom are the best backstories in OP for me. Water 7 was probably funnier. Water 7/CP9 had a bunch of epic moments that got my heart going (eg walk to Franky House, gattling gun, Luffy/Zoro freeing themselves from the buildings, maybe Luffy using 2nd gear the first time), Arabasta had one (Gomu Storm) but mostly it just had cool moments (eg Ace's powers and Zoro vs candleotoko). Both had the SHs getting fucked up, with Luffy completely losing to and nearly being killed by Crocodile being the bigger WTF moments. Luffy beating Crocodile was more inspiring. Water 7/CP9 peaked early, then fell off a little, then peaked again (End of Lucci-Luffy, Buster Call, Sogeking, Merry's death), whereas Arabasta was a perfect build to a crescendo.
Going Merry turning up on its own was a great moment. They already set it up in Skypeia (favourite pre-Marineford standalone arc, at the time. Fight me) and earlier in Water 7.
tldr don't know. Was gonna say Water 7, but now I'll say Arabasta.