To directly answer your question, the UX you (and I) observe as poor is the result of cheap available technology. It was NOT intentionally designed for the best UX. It was designed for business (cost) and technology-simplicity reasons. Arguably that detail of its UX wasn't designed at all.
Actually, at the time 3-way switches were introduced, to be able to control the lights from two locations would have been an incredible UX improvement at the time. Before that, there could have only been one switch in one of the locations, meaning you would be ascending or descending the steps in the dark half the time! To be able to "remotely" control the lights from another location was a big improvement- so much of an improvement that the lever being in the wrong position was a minor "cost" for such a big "benefit".
Back then, if someone wanted to be "apple like" and provide the great UX you and I prefer, they could have built a relay control scheme I describe below. But no one bothered (maybe one or two millionaires or institutions sensitive to such annoyances did it?).
The low-tech great-at-the-time "3-way switch" solution has stuck ever since. It was also relatively cheap to add to the switch manufacturing process, which helped its adoption greatly.
Life is full of these sorts of "early optimizations" that now, in retrospect, seem like poor choices, especially from a UX point of view. And the "installed base problem" prevents a quick upgrade to a newer better solution.
-- technical explanation --
Examine the wiring. In so-called "3-way" wiring, each switch does not function as on/off of a single circuit but rather as "alternating a common terminal between A and B terminals". These are cleverly wired such that the A and B terminal of each switch are wired together A-to-A and B-to-B and the actual circuit is controlled between the TWO switch's COMMON terminals. Thus the circuit is closed - the light is On - only in the combinations of switch positions AA or BB; in position combinations AB or BA, the circuit is open - the light is off.
you can achieve what you desire by using modern digital networked switches where one switch is actually the real switch, switching the load off, while the other is merely a remote controller sending a command to the real switch. You can setup such an arrangement by using two Insteon switches inter-programmed with each other (about $50 each) or using Z-Wave or ZigBee. The UX of the Insteon units is what you want-- toggle switches where pressing the top definitely always turns the light on, and pressing the bottom definitely always turns the light off (or the other way around if you are Euro and mount them upside down).
In pre-digital technology, you could also build your own comparable user experience by using two independent momentary-On pushbuttons at each location, or ideally on a physical rocker switch that spring-loads back to a middle neutral position "momentary SPDT or DPDT switch"), wired to two mechanical relays, one of which self-energizes itself ("locks"), the other which releases the first one's lock.