I've always had a fondness for 'oblique 45', but there's no
real pros or cons to any of the projections, except keeping it at horizontal where it's a lot less work obviously.

Congo Bongo has used all kinds of projections, depending on the port, so I was looking at screenshots to see if any were better for depth vs height, but I couldn't really notice anything significant. These kind of projections are definitely more interesting to look at when there's lots of height levels though.
Control is a bit annoying for me if the joypad axis is rotated (ie. up goes map-north vs away-from-the-camera) and perhaps the inverse is true for other players, but that's up to you, and not hugely problematic if the indoors parts aren't action orientated anyway.