Funny thing, I have the Ultimate Edition (haven't heard the 1999 Album), and I'm a big fan of the Escape from Naboo cue, which was also used on "Anakin Defeats Sebulba" (that is, in the Ultimate Edition) and later during the battle on Geonosis in Episode II and the descent of Grievous' ship in Episode III. Is that cue in the 1999 release? Because that's a pretty darn awesome theme by Williams, one of my favorites in the prequels. If it wasn't included on any of the soundtracks, it makes the Ultimate Edition a fine purchase.
No it is not on the OST album - i suggest you find another thread i have made where i have analysed the UE tracklist and marked the unreleased cues with a * for "Unreleased" and ** for "unleased music within cue."