Lon Lat Lon Lat
Lat/Lon is really the standard. The fact that some software internally represents it as Lon/Lat doesn't mean it's not a settled issue. If you look up the coordinate of a location - it's always in Lat/Long. You can't rewrite all the books and change all the maps to make it nicer for programmersAs the linked post says, Lon/Lat is generally easier to deal with b/c it matches to X/Y (and the North/Up way we look at maps). But you still have annoyances. For instance Lon goes 0-360 but Lat goes -90 to 90. This is also mathematically inconvenientAdd on top of that the X-Y coordinate on images generally have the X flipped and starting at the top left corner. So changing to Lon/Lat doesn't fix everything.What I personally lean towards now is converting everything on read-in to a South/East coordinate system so it matches the flipped X-Y of images (like GeoTIFFs) and just always working in that system. Image manipulation, drawing to screen, output etc. - those systems/libraries I can't really modify myself. Everything else I can manipulate in whatever coordinate system I want. So it makes sense to choose the most convenient. Plus only dealing with positive coordinates is a big plus.That all said, I'm a total noob and I have no "geospatial" background (just writing some software to deal with rain data right now) So this isn't pro advice.  I'd just be curious what others think