Nik may be going nowhere, but that doesn't affect Capture NX. CNX is owned by NIkon, not Nik.
I use the Nik plug-ins also, as well as onOne's. Since either will run in standalone mode, you can easily use them with CNX using the Open with command (there is even a little CNX plug in that will let you pick which program to open with on the fly) or you can use Photo Mechanic to open a file into one of the stand alone plug-ins.In either case, you can edit a tif or jpg in the plug in. The latest onOne Photo Suite will even open NEFs directly, but without any of the camera setting reflected in the image.
I also use DxO Optics Pro a bit, but generally for some bulk batch correction and processing.If you think CNX interface is quirky, wait to you see DxO! Plus, except for their own Film Pack, there are no plug-ins that directly work with Optics Pro.
Of course, CNX will use the cameras vignette control setting, if available, or a separate vigneete control. In addition CNX can apply distortion control for Nikon lenses, either via the camera setting or separately.
Of course you need to use software and workflow that you a comfortable with and understand, but for the situation you describe, I think a PM/CNX combination would meet your needs.
I doubt if going to JPG will give you the flexibility to do what you want. It would be simple enough to try shoot only JPG for a week or a month and see thawaht you think.