There are whole books on passive design.
Lawrence Livermore has a simulation program that can help with design.
Some quickies: for a south facing window, triple pane is net lower than double pane. You lose more from the extra glass than you gain from insulation. It’s pretty close though. On the shaded (north) side if the house triple pane is a win.
Gas leaks out of sealed units. Typically 5-10 years. Argon fill may be worth it. Xenon not so much. Do they make windows that can be refilled in situ?
The year is not symmetrical. April 21 is one month after spring equinox and you want heat. August 21 is one month before fall equinox and has the same sun, but heat is the last thing you want. Consider crankdown awnings that allow you to adjust.
There is an edge effect with windows. Both the window frame and the rough opening are locations for higher heat loss. Consider the window to be 6” larger all the way around for heat loss, but only its real size for heat gain. I would not install a window smaller than 3 feet on a side except in a bedroom or bathroom.
Skylights have higher losses. They aren’t close to normal (right angles) to the sun in winter, unless you have a very steep roof running east west. They get covered in snow. Air temp at the ceiling is warmer than room as a hole. More loss.
But the biggest reason is that it affects the whole roof design. You can’t put 2 feet of cellulose insulation by a skylight.
Look at clerestory windows for a compromise solution. These still are the highest point in the room, so will have higher temp air. (And triple pane may be worth it.) But in our climate they are close to normal to the Dec 21 sun (13 degrees above the south horizon at noon) and so still do some gain, as well as provide daylight in the northern half of the house. In addition they are more insulation friendly to the roof as a whole.