people are much too much in love with the idea of timbo the auteur. the best songs on timberlakes first album were always the ones by the neptunes. rock your body, like i love you, all instant classics imo. i think timbo will always be preferred by dance music fans or people that like their R&B/rap producers to be firm auteur figures for his colder sonics and generally less R&B elements - cry me a river is def much more european than the neptunes songs. basically, timbaland might be a better technician or producer, but the neptunes have always written better songs. timbaland as a producer always has to dominate a track with his name on it. pharrell might be a bit of a punchable poser but he at least knows how to write good pop/R&B songs. timbo does good beats.
I think the big difference is, the Neptunes songs on Justified were pre-assembled, where "Cry Me A River" is a joint operation between Timothy, Justin and Scott Storch (reportedly).
Neptunes are great songwriters, but that's the thing, they have a deliberately musical approach, whereas Timbo comes from a more off-kilter, rap producer... His whole R&B thing comes from being picked up by Devante Swing and being modeled AS an R&B producer, for working with R&B artists. It's very close to the Prince formula I was describing... He's at his best when the talents surrounding him (Missy, Static, Danja, whomever else) are able to provide him with a sort of conceptual spark. Also, it's telling that the one person who was always at home in his songs was Jay-Z. He never had to figure out how to craft songs around these gimmicks, because all he had to do was find the beats and work around it.
Discussing Neptunes Vs. Timbaland is easy to disrupt though because Tim OBVIOUSLY inspired the Neptunes whole "inorganic" obsession. Before they were either interested in constructing tight little grooves, and they were funky. But it wasn't until post-Timothy you started hearing them mess around with these unusual samples and noises. I do believe Timothy provoked that in them, that such weird little things could be the very thing you could base a whole song around. A song like Ludacris "Southern Hospitality" comes to mind.
Also interestingly enough, so many Timbaland rip-offs, progeny, admirers... Darkchild, Bangladesh, Polow Da Don, Danja, etc. But who are the Neptunes babies? Obviously you have underground artists like Tyler, but I can't think of new rap producers who ever modeled themselves stylistically after the Neptunes sound. At least off the top of my head.