The shorter jar is much better. It's wider at the bottom with a wider blade. This allows for more efficient blending and better "chopping control". It's also easier to get things out as well as clean. The models that come with the new jar (7500, 750) are also the quieter models, if that matters to you.
If it's about smaller portions there is little to no difference between them and if that is important then the smaller 32 oz container (works on all models) is what you want.
There really isn't that many different models - it's just that there are several models that have different names and numbers for marketing purposes. It is darn confusing - even talking to folks at Vitamix doesn't always help.
This site: http://gotgreensrevolution.com/ has an amazing amount of info to help. Contacting them was the best thing I did as they gave better info than Vitamix did. I now have a reconditioned 7500.
Basically there are:
New Generation Series
The 6300 is the exact same as the 500 which is the same blender as the 5200 with added programs. It is not any quieter than any of the C-Series and "adjustment based on size of vegetable chunks" is made up.
Basically decide if you want programs or not (personally, i find the beauty of a vitamix to be the variable speed and don't care for the cycles). Then whichever you decide - get a reconditioned version of it through vitamix. Basically the same as new but at a huge savings.
Ultimately you can't go wrong with any model.
according to Vitamix - they do not honor warranties for machines sold on ebay