Taking the Padrons as an example. Many people state they like the Padron 6000. From what I can find the 2000,3000,4000,5000,6000are all made from the same tabacco with the only diference being the length and ring size. This seems to be the case with many cigars. What am I missing?

I don't know about the Padrons you mention here per se, but most manufacturers will put out 'vitolas' of a line. For example Partagas makes the line 'Black Label,' which comes in different sizes (vitolas), which are, as you said, the same tobacco but in different lengths, ring sizes etc. In reality the different vitolas of a line can have strikingly different flavors and smokability, due to perhaps different ratios of filler, wrapper etc., but then in other cases the different vitolas taste the same or similar.

I think the key is, like primate said, different ratios of wrapper to filler to binder.

But also, construction may differ due to the different size or shape.

With thicker ring gauges, a blender can be more 'creative' with the blend, as more tobacco is utilized. Also, a cigar can build in flavor and strength as the tobaccos and oils burn, so a churchill may seem more complex than a robusto. One exception to this rule that I've found is the CAO Brazilia. The smaller sizes seem to be the most flavorful, and fuller-bodied. But that's just me and my crazy taste buds talking.

A great example of a big difference with vitolas are the Joya de Nicaragua Antano 1970s.

The little Machitos (my favorite) have a very spicy taste with every puff imho. The larger ring and longer length Belicoso, which still a great cigar, has a more subtle taste.