Hi there,
I haven't done either of these tours with JY, but I have travelled quite a bit in Vietnam, so here's my opinion, for what it's worth - I think to visit Vietnam and not visit Saigon / Ho Chi Min City, which apparently is missing from one of the tours, would leave quite a gap in the understanding of how Vietnam came to be how it is now. Okay it's not the most beautiful of cities, but it offers a real insight in to the psyche of the country and its people, and you get a good understanding of an important aspect of fairly recent world history.
Hope you enjoy whichever trip you decide to take!
RM.