What would go a long way towards solving the issues with node-webkit would be to maintain support for the last 2~3 versions so that developers would have options at export when/if something breaks.
Take the current situation with node: v0.11 inherited terrible frametime consistency (janking, jerking, whatever you want to call it) from chromium v38. Now, rolling back to the previous version (0.10.5) fixes this. All is well and good, right? Not exactly...
The problem is this: if some change to C2 breaks compatibility with the older node-webkit, Ashley isn't likely to fix it ('update to the newest version of node, we don't support that version'). This leaves us SOL until a new node rolls around that works better. Or, we have to stay on an old version of C2.
Ultimately, unless you are literally coding your game from the ground up, you have to place faith in something: an engine, a set of libraries, etc. No choice will be without problems.
Likewise, if you are aiming at multi-plat developement, some platforms are going to be much more problematic than others (Linux, Android).
But for C2, I don't see any reason not to maintain some level of backwards compatibility for node-webkit. After all, it is our ONLY desktop export option.