People are different, and no control method is better than the other for everyone.
Each one has benefits and weaknesses.
The mouse and keyboard has better camera control, aiming and direct access to signs etc.
You can also select only the loot you want when you are searching rather than being forced to take everything at once.
You also have quick-save and direct access to panels.
However, as dodging is a huge part of this game, it's much more intuitive dodging with a controller's analogue stick than pressing keyboard buttons.
And with the radial menu, direct sign access although handy with a keyboard, isn't that big of a deal with a controller.
QTE's can sometimes be easier with a controller, but that depends on which button you have to press.
At the end of the day, there is no right method, it's what works best for you and your play style.
Personally, I use a controller, but I lean over and use my keyboard for quick-saves and panel access etc.
I'm too lazy, but an ideal solution is to use Pinnacle and create a controller profile with all the handy keyboard shortcuts.