I know some people have bought a set (new or used) simply for the build experience then resold the kit down the road as a whole or parted out. I can relate to a degree as a number of my purchases were more for the build itself while other times primarily only for the pieces. Moving along.
* Does keeping the plastic bags increase their value?
I do not believe so. That plastic may be part of the original packaging but once it is sliced open even with a pair of sharpened scissors, it's inconvenient waste. Since most everything is numbered anymore, you could keep the front of each bag as a means to label every storage bag of parts assuming you willingly want to go through the extra effort of sorting out all the pieces as per the instructions. I see this less of affecting resale value and more along the lines of receiving potentially better feedback.
* Keeping the extra pieces?
So long as all the pieces to completely construct the set in its entirety is there, buyers should be fine. While sites such as BrickLink do confirm a general list of expected extras (when the kit comes straight from the source), those numbers are not infallible. Plus, no one can keep track of what extras they actually did get with the set versus what is listed. I would consider the extras as "pocketed parts".
* Negative feedback for smudges from greasy fingers.
You can clean the parts before packing for resale leading to potentially better feedback. Usually, buyers do this themselves when going for used. Fingerprints on pieces is kind of expected. Unless we are talking about the amount of grease I could use for coating a frying pan to cook eggs or the kind thick as peanut butter, you should be alright. People can be pedantically picky but there is only so much one can do.
Mind you, these are based off observations and personal opinion rather than genuine experience. I am just a builder who typically buys new that has been here for a very long time. Haha.