Yes a big big difference.
The Arcade Banjo Kazooie is simply the N64 original, running at a higher resolution.
The Retail Banjo Kazooie is actually Banjo Kazooie 3. A brand new HD game developed exclusivly by RARE for the 360.
Banjo Kazooie : Nuts & Bolts focusses not only on the platforming of old school (which mostly takes part in the large HUB world) but on building vehicles lego physics style and taking on challenges in the off world areas of the central HUB. There is an amazing amount of versatility involved and it's great fun creating new vehicles or obtaining that special part needed to finally take to the skies, or seas.
I know you enjoyed the original Viva Pinata, maybe you should give the sequel a spin. It's very much improved on the original, and just as absorbing and enjoyable.