I do get the argument for Timbaland being more soulful. I think there's three elements that Timbaland pours into his production that makes it more soulful and timeless:
1) Organic sounds. Whether it's him beat boxing, the crickets, wind chimes, etc. he puts natural elements into his beats that add to the atmosphere
2) Drums. There are few if any producers that rival Timbaland's drum programming. You can have the craziest sample, but if you throw some mediocre or wack drums on it, it will sound horrible.
3) Live instruments. Reading through some of the credits to some of Timbaland's best productions, a lot of them have live instruments. it might be just me, but this is also true of The Neptunes' best music. The N.E.R.D. albums are heavy on a "live" sound and In Search Of... is their best work IMO. Then comes Kaleidoscope and Lord Willin'.