Here is one I must make immediately for anything else to go in place: Flooring choice.
The house: 1970's, dark and dreary
The room: A 1st floor 14 x 11.8 room. It will be a study/tv room.
Current floor: Carpet that must be ripped out.
New Floor: Oak (probably red)

Here is one of the challenges. The room is off a hall which has a mix of walnut-pegged red and white oak planks alternating 3.25" and 2.25." Originally this hall floor was dark, but a few years we had it sanded and restained a lighter golden honey.
(See for a similar floor )

The hall's floor planks run perpendicular to the door opening.

We don't want, nor can we afford to try to match the pegged wood, but the house is already chopped up enough with different flooring types, so I'd like it to be similar enough to "flow" visually.

We have decided on oak and the flooring installers suggested going with the red oak and staining it a warm color to make it similar to the ajoining hall.

Our decision difficulty is whether we should use 3.25" only or alternate it with the 2.25."

The plan is to lay the flooring perpendicular to that in the hall because of the joist direction and because we figure that since we can't match the floors, we should clearly define that we aren't trying to by laying the planks in a different direction. (Also, I like the floors running the lengthwise of the room)

The disadvantage to alternating the widths are a slight increase in expense and possibly that even with the wood laid in a different direction, it might still visually seem like we had "forgotten" the pegs in the room.

But, I want the look to be as unified as possible. Does this make sense?

I would appreciate your thoughts. I have no ability to visualize what I can't see.

Here is a picture of layout of that part of the first floor with the study in yellow at the top right. (The room to the left is a bathroom with grey tiles and.....a sliding pocket door opening into the study. Awful, I know)

From Blueprints, Interior

It looks like from your plan that you are not going to have much of a view of the floor of the den from anywhere but the doorway. So there won't be a long panoramic shot of looking at the contrast. I would probably not worry about the pegs or the alternating widths and concentrate on trying to get the tone as similar as possible. If you are really worried about it, maybe consider putting a beautiful hallway runner in the hall area in front of the den door. Even if it doesn't cover the floor in that area completely, it would detract from the difference (if it really bothers you after it's laid). Remember, when you get furniture and people in a room, things like that really fade into the background.

So, using 3.25" instead of alternating 3.25 and 2.25" shouldn't really make any difference in this case?