That's a good idea. If you painted it directly on the inside of the clear plastic it would look very nice and shiny, and would not get damaged easily. There are some problems however. If the paint starts to peel or if you want to paint the house a different color, it will be necessary to disassemble the windows. It might be possible to design them such that disassembly isn't too difficult, but it would require a lot of redesigning. They also might be too expensive to be popular.

Although this sounds good, you've forgotten that dirt, bugs, spiderwebs, etc will certainly get between the window frame and the plastic channel.

You'd have to look at it all of the time, with no ability to clean it unless they designed them be removeable, which would be difficult and add cost.

hrnech is right about the dirt and bugs, but there are plastics out there that retain paint--I've painted or stained vinyl siding and trim for years and it never comes off. Or perhaps a soft, paintable weatherstripping/paper strip could be inserted behind the channels, with the top and bottom of the channels being sealed with the strip folded over top and bottom. Stops, as in old windows, would hold the whole unit in place.