The contractor suggested to use clear oil poly(no stain) on red oak. He said it would look nice.
Another alternative he suggested was to use Pecan stain with oil poly I believe.

Would pecan color with oil poly look better than the just clear oil poly on red oak ? Would the pecan color with oil darken more than just clear oil ?

Or would Pecan stain look better with water-based poly ?

Any suggestions are appreciated !!!

Thanks

Have your contractor make samples for you. Color is very subjective.

Your question is one of aesthetics, so there is no right or wrong answer. Some people prefer (myself included) the look of a natural finish, others prefer a darker tone.
Traditionally one would stain a lower grade of wood to achieve a more consistant (but darker) tone or perhaps to match some other element in the space.
But it really boils down to what YOU want the floor to look like.
A water-based finish will have a "washed-out" look on top of the stain, unless you use a a tinted first coat or a hybrid finish such as "Emulsion".

Thanks, for the replies.

I'll ask the contractor to make a few samples. But it looks like I may go with the natural clear poly probably with semi-gloss. I like how the old wood looked with a nice amber color.