I have to believe that 32GB of storage would probably cost Apple today, what 16GB cost them a few years ago. It would stand to reason, then, that the 16GB of storage in the "low-end" model probably costs them next to nothing.
I've hadd sluggish performance on my iPad 3 since iOS 8. I'm not sure why you thought iOS 9 would improve on that. OS X Daily had an article, and they actually recommended against upgrading the iPad 3 and a few other older units. Here's the article: http://osxdaily.com/2015/09/14/prepare-for-ios-9/
Give me more places that take it, and consistency with how the transactions are handled. However, with the rollout of the 6s and 6s Plus, we'll at least see a dramatic increase in the number of iPhones compatible with Apple Pay.