Justify content and Align items operate on the Main axis and the Cross axis respectively. By default this would be the horizontal and vertical. Because of the flexibility of the layout system you can tell it to distribute the main axis vertically instead (flex-direction: column) which would make the cross access horizontal. There is a consistent logic to this which affords a lot of power when creating layouts.
The current layout system is designed with language (and content) direction preferences in mind. Could you expand on what you think an ideal layout system would be? I'd be interested to see what an alternative would look like with the same considerations.