There probably isn't any way to have the mullions look pristine from the inside since glue is glue, but you might try applying pressure on the mullions with a roller yourself to get a little better adhesion.

Glass was also taxed on size in some areas (mostly in Europe) so the way to cheat the tax man was to use smaller pieces of glass which were less costly tax wise. (This was particularly true of mirrors which were heavily taxed). So it was both initial cost and cost later :) Just like us today LOL Windows were also made from the bottom of glass bottles in many places in the country. You see it on occasion in England and in original window's in cabins in the US (my grandfathers place had a couple). They were a poor man's glass window. I'd take a couple things into consideration in choosing. Style of house, and what you're blocking with the extra wood. In my home, I'd never want the smaller glass expanses because I am on a lake with fabulous views. I don't want tiny squares of lake...I want huge expanses of lake (some of my windows are 6'x8' picture). I'd never want to change that to fill a style desire :) But in some homes...the view is not a main feature, so I'd think about what looked best on the house, before I'd consider the view out of the windows.

Hi JDS, With the Colonial revival I wanted to use an example that showed the grids proportionate to window size vs. same grid height. The window mullions where already designed but I changed window manufacturers and now specifying the exact heights, which was 1/3 of glass opening. Now that we're getting into the details wanted to get feedback if there was a standard height for casement mullions for a craftsman style home. Is it just me or do the lower windows with the same grid heights as the smaller windows look odd?

You should absolutely do the first option (4 lite in both the door and gable window). The front door is the most important statement piece on the exterior of your house, and while it the difference between a 4-lite and 9-lite doesn't seem huge on paper, in person the 4-lite will be draw praise from everyone that walks through it. It's a striking and interesting look that also coordinates with the other windows on the house, not because the lite sizes are similar, but because colonial (or equally divided lites).