Ashley , The problem with replacing animation sequences directly into the C2 created folders is that the images have all had their names replaced to a generic 000.png - xxx.png. If I have my run animation originally created as run000.png - run012.png , am I expected to export all of my new animations and images with the exact same file names sequence of 000.png - xxx.png ?
If you don't want to change the IDE to allow external asset reference then one easy solution would be to allow a multi select of all of the animation frames, which would then allow you to delete them , and then reimport the new sequence. Currently you can only select one frame at a time to delete. Hence why I create a new animation, import the updated frames into this, delete the old one and then rename it to the original. Yes, it is as tedious at it sounds. At least implementing a multi select via a marquee select of frames would be a halfway measure.
The problem with updating sounds in the folder is that we have to replace not only the original wav file but also the ogg and m4a files. This means to you have to use C2 to import the original wave file, but for any updated audio files, the user must manually convert to ogg and m4a to replace into the folder structure. At least the wave file has not been changed by C2 upon import.
One possible way around this would be have the option for C2 to only do the conversion to ogg/m4a on preview/export, so only the wave file needs to be replaced. Yes this would slow down the preview process, but would be good to have as an option. Even better is have C2 only reference the audio files from a folder of my choosing, then I can replace the originals at will.
Another issue with replacing sounds is that if I delete a sound , any actions using this sound are automatically deleted without any warning to the user! This caught me out quite a few times initially. So the workflow becomes import the updated sound (which of course gets renamed!), have it converted, changed the actions to reference the newly named sound, then delete the old ones. To compound this, since I can't multi select sounds in the project view, every single sound needs to be put into a folder so that all 3(wav,ogg, m4a) are in one folder to make it easier to delete. Yes , it is a currently a nightmare. My current C2 game is a musical one, where every sound has each 7 notes of a C major scale, so each time I need to update a sound it is quite a nightmare!
On a related note, is the general way the C2 needs all assets within its own directory structure. If I want to iterate my project to the next version (which I tend to do several times a day), this means that all assets have come along for the ride. If the project has 250mb worth of assets, each time I save my project it is saving all the assets, where ideally all I want changed is the project file that will point at the same assets. What is I want to go back to a version of the project that I did the previous day , but with my updated assets?
Hopefully, you can begin to see that separating project files from assets is the only way to go for a decent sized project. Sure, there is a certain elegance in having everything contained in one zipped capx. This will work fine on a crappy bird clone, but for a project with hundreds of sounds and sprites it becomes a logistic nightmare.
While I don't have the game industry experience of 
stuatk , I have over a decade of experience in the broadcast animation business and have worked on many high profile jobs. All compositing and editing packages only ever reference media files for good reason. It makes it easy to update/reload files at their source and the small project file is easy tranportable.
Just the fact that someone of stuatk's calibre is even trying out C2 is noteworthy of itself. C2 has been turning heads, mainly because of its event system which is the jewel in its crown. Since it is so good, users expect the rest of the software to be of a similar quality. Sadly the asset management, exporting problems (reliance upon 3rd party solutions) and non modularity of code are the main issues which will continue to plague the product unless they are addressed.
Hopefully the Scirra management will take note these issues in its long term business plan, as there is now plenty of competition among engines now. Most offer a free (Unity and GMS) or very low priced(UE4) version and they don't tend to have the same issues. Although there is nothing out there that is as easy to use as C2, there are plenty of contenders such as Stencyl, GameSalad and Game Develop (which was recently open sourced and is very close to C2 in terms of workflow), who would happily eat Scirra's lunch. I would prefer to see a more pro orientated version (C3 Professional) with haxe or similar underpinnings (ala Stencyl) be developed in tandem to the current C2 which would stay as a html5 engine.