If you’re talking about a GUI that, among other things, hooks up to UCI engines, such as Stockfish, almost any chess GUI will be better than the Stockfish client you’re using.
Particularly for the Mac—though not limited to the Mac—I think the new-and-improved “Pro” version of HIARCS Chess Explorer, namely “HIARCS Chess Explorer Pro” (HCEP), is excellent in many dimensions, including what you’re focusing on. HCEP has an optional column-based view of the main line and a really nice way of not only indenting variations but also labeling them to make it clearer where each one starts. (So it satisfies your “One line per move pair. Indented branches, one line per move pair” desire.)
It integrates very nicely with Stockfish (or any UCI engine). For example, if you hover over a line of Stockfish analysis, a picture of the resulting chessboard follows your mouse cursor as you move along the line.)
And, to address another desire in your post: It allows you to add annotations.
But, more generally, it’s arguably a ChessBase killer. It now (i.e., as of the Pro version) reads ChessBase databases. And it searches large databases (e.g, the CB MegaBase) blindingly fast. (People say it’s much faster than ChessBase itself, but I can’t compare since I don’t have ChessBase on my Mac.)
I’m not associated with HIARCS, so this isn’t a promotional post. (I did beta test the Pro version when it was first being released.)
HIARCS Chess Explorer Pro is a paid app. If you want free, SCID vs. PC is open source and has a Mac version (look for “ScidvsMac” in the download list). It’s a very capable GUI, too, though a little quirky as open-source projects can be. It has a proprietary database format and doesn’t interoperate with ChessBase databases. (Last I checked, it was not and likely never would be compatible with Chess960 games.)