For iPhoto users there are plenty of options. Keep Photos for syncing only once iPhoto bites the dust (never thought I'd say a kind word about iPhoto).
For C1 and Nik: In C1, choose "Export Variant", and set your export folder. Before exporting, select "Open With" and choose the Nik plugin of your choice. Exporting the variant will open it directly with the selected Nik plugin. I believe C1 has an auto import from select folder option.
Not much different than Aperture, or I believe, LR except you do the export.
I also went back to iPhoto. What a relief. How Apple could have released this mess is beyond me. The very people it's aimed at can't understand how to use it (for good reason). The people who it's not aimed at know how to use it and avoid it. Great market strategy if you don't want to cater to photographers of any kind.