Is a bottom end Martin a better guitar than a mid, to top range guitar from other manufacturers?

An impossible question to answer. It would depend entirely on who the other manufacturer is. But, since you mention Yamahas... IMHO Yamaha's better guitars are at least as good as any Martin priced below the Standard Series (D-18, D-28 etc.) and some folks think that their top-of-the line guitars are as good as anything Martin makes.

Bruce