I totally agree that load time would make a custom app like that painful -- and in order to support animations, the app would have to have some sort of extension / built-in support for data exchange. I'm cool with that, if that's an option on the table, and if it's not, then I have another suggestion that might be even easier to implement:
Have import/export formats which allow us to put out entire animations / directions / spritesheets / whatever from a single file or set of files. MMF has this, and it's had it since CNC but the support has been awful and the importers have all sorts of problems with crap like transparency, bounding boxes and the like. Again, when I was working on my own sprite editor, one of the key features for using it over the built-in editor was to be able to export to the clipboard (for single frames) which replaced (0,0,0) with (8,0,0) and transparent with black cause that's what MMF wanted, and animations as bounding-box strips for it's "multiple frames" importer. This was extremely useful for the few people that knew how to utilize it, despite the bugs, and I think it would be very easy to implement a similar feature which would be unobtrusive and an excellent alternative to copying/pasting everything in an AO by hand.
I doubt the feature was used much because they never fixed any of the bugs with it, and it was hella annoying. However, this sort of import is perfect for making everything in a different editor, because then all the programmer has to do is write an export filter for it (in the case of existing software) or build in an exporter into their own program which will take an image/animation format Scirra likes.