My first choice would be to put hardwood flooring throughout. If you can come close to matching the existing hardwoods, but not quite, then you could use a 9" stripe of a much darker wood as a border around the new area, thereby separating the old stain with the new and almost matching new stain. They used a narrow version of what I'm talking about in the photo below.

Try to match the hardwoods. You won't be sorry. The look will be much more cohesive.

I forgot to mention that the ceramic tile floor had been built up ( since it was laid upon linoleum )and the hardwood is now lower than the tile. Yikes!!!!

Rip it all up first. You need to make sure your subfloor is ok before putting anything on top. If you are going to do this job then do it right.