low e glass is the norm in windows, will your plants really benefit from sitting on a window sill? is it the look you are going for... it's your home, make a sill.

Group your sun loving plants together and make an appropriate sunny location to show them off.

if your bathroom or hallway ends, as you said, are the best place for your plants, go for it.

@Lyn Nielson oh yes, low e-glass and anti-uv coat...I am not sure if this would affect the plants on the sill. Others with sills?

Without knowing what the windows are going to look like without sills I can't say for sure, but I'm thinking that if you have them on one window in a room they should be on all of them. I'm also not sure how I feel about having them in one room, but not another. I think for me it would be all or nothing.

Consider plant stands the height of the window sills to place your plants on.

If you want them for plants you could use a counter top material instead of MDF or wood. Your contractor could have them installed or you could do it after you moved in.

Is the house traditional, transitional or contemporary?

@aziline countertop material sounds like a nifty idea. I didn't know it was a DIY project! @cpartist the house is transitional.

How wide will the sills be, how big will your plants be, what kind of window dressing will you have that might interfere (e.g. blinds, curtains)?

I was thinking about small pots no larger than 4". Planning on Roman shades for window treatment.

IMO house plants in 4" pots are in pots too small to grow so I would do plant stands instead . Maybe do one nice deep one for above the sink for herbs but honestly too many tiny little pots just look like you have not transpalnted from the plant store . Also most plants need sun so think about how that is going to be done. I like solar shades more than glass to control UV if you want to grow plants

Small plants on window sills? Only if it's a cottage look you're going for in a home. There are other ways to display small plants effectively. Larger plants have a more sculptural effect in a room.

Thank you, @BeverlyFLADeziner! These are awesome ideas that can go close to the window, not necessarily on a sill. I like these ideas.