Don't be so critical of yourself. I read the best filler is to use wood dust/shavings from the wood mixed with wood glue to hopefully provide a similar match to the wood. However best not to use the initial shavings as they are likely dirty and leave you with a brown colour.
Reason you have darker brown colour wood in some bits is probably because they haven't been touched with the sander much.
I found when using the big floor sander in our living room (4m x 5m approx) and did a pretty decent job. Just have to make sure you hit all of the spots. Did the 2nd reception and made a pig's mess of it as i rushed it as the girlfriend wanted it done asap as it is the kids toy room.
Quite a satisfying job when it comes out well. When it doesn't.. well there is always carpet