You could submit an issue or a pull request with suggestions on what a more obvious UI might be!
SourceTree is much better in this regard.
UI is same as Tower. Doesn't seem that far off for me.
No, Tower works differently (unless it has changed in the few months since I used it). In Tower, you can select lines by clicking line numbers, but then you must click "Stage" to actually stage those lines. Then your selection is cleared and those lines are moved to a separate "Staged" tab for that file. Whereas with GitHub Desktop, just selecting the lines marks them as lines to be staged. (GitHub Desktop doesn't actually run `git add` on those lines until the moment you click "Commit".)
Looks exactly the same as the previous GitHub Desktop app.