So why does there seem to be more fuss about colonoscopies vs upper? is it more to do with the preparation required and the chance of incomplete exam?

Colonoscopy.: Not sure what you mean by "fuss," but it is true that preparing your colon for a colonoscopy is more difficult than just not eating after midnight to prepare for an upper endoscopy. However, if you take the preparation properly, more than 90% of colonoscopies are completed without difficulty. Just follow the instructions that your doctor gives you and it should go well. Good luck.