I totally agree that the full-stack offering can be rather off-putting, but the business side of DS still doesn't understand how to reliably make money from this market. Cloudera (and friends) have made money from a full-stack offering, so it's easy try to imitate this success.
IMO the online IDE is very useful for expositions and small projects, but indeed a limiting playground for larger projects. I'd love to see SAAS/PAAS do better at co-locating their offerings so that, e.g., I could run part of the stack on my own hardware (which is where the data lives). Perhaps Docker would help facilitate this business model.
We know that there's room for improvement on some workflows, in particular Git interop, but we have our sights on a platform that plays well with as many others as possible. Please ping us with any other thoughts you may have!
Or do you want more utilities that work together and run locally? (i.e. repeatable workflows in project bundles of scripts + data + saved notebook logs etc).