Manual Camera and Camera FV-5 are top choices. Manual Camera has more modern UI (FV is said to have its ui rehauled soon too, it also has terrible shutter sound lol).
When it comes down to features both have everything manual one has + everything camera api 2.0 provides with (which is Raw file saving, manual focus, manual shutter speeds).
For Nexus6 however both have colour balance act funky, might still be api's fault and should be fixed soonish.
I wouldnt remove stock camera's hotkey from the screen tho - it is amazing for when you need to grab a quick auto photo, also HDR+ on stock is amazing for night photos.
Ok since what I wrote might seem tad chaotic, here's a list:
STOCK Camera:
Good colours
Good auto photos, and I mean it
Great(for a phone) night photos with HDR+
Terrible photos with flash
Bare minimum when it comes for options
FV-5 Camera (my favourite)
Has all the manual settings when your phone supports them
Tries to emulate them when it doesnt (like fake exposition, which sucks tho, or RAW saving on one plus one that doesnt really support it atm)
Saves photos to its own folder
Raw support, loseless compression png option available
Colour balance works (just checked)
Very responsive developer
Lots of updates
UGLY UI
TERRIBLE SHUTTER SOUND
Important Edit:
Just received playstore update to newest (beta) version of FV-5 Camera (what a coincidence lol), UI is better now, still not as pretty as Manual Camera but less cluterred and quite OK, they also changed shutter sound to something much better
Manual Camera:
Has all the manual settings when your phone supports them
Saves photos to same folder as stock camera, personally dont like this
Raw saving when supported
Awesome UI and sound
Still didn't get response from developer (sent mail like 2 weeks ago)
Somewhat updated
Broken colour balance
Photos for comparision:
NOTE: Unfortunately i do not have FV-5 examples at the moment since I was testng manual cam recently. I will probably do some FV-5 testing after the ui update (and hopefully will change that horrid shutter slam).
Somewhat reddish photos are from Manual cam, natural colours from stock cam with HDR+ on. Photos without a tripod, so if they are blurry its because of me breathing and not standing still enough
Camera app comparision - Album on Imgur
Wanted to upload here but images are too big and i dont really have time now to resize, so posted link instead ^