Short answer:
You can get pretty close with the rocket equation and optimizing for a rocket of given mass to lift a maximum payload to a specified velocity.
Long answer:
I finally tried some math (though in a slightly different way than the link above).
First, I made the problem dimensionless
- dividing all masses by the total mass of the rocket without the payload. The mass of the rocket is then equal to one.
- introducing a factor $\phi$ which equals the total mass of the first stage divided by the total mass of the rocket. $\phi=0$ would mean a zero stage of no mass (rather silly) and $\phi=1$ would mean a second stage of zero mass (equally silly).
- Calling the dry mass fraction of the first stage $e_1$ and the dry mass fraction of the second stage $e_2$
- Assuming a mass $m_3$ which is the payload, which comes on top
- Dividing all velocities by the target velocity $v_t$ (in this case, needed to reach LEO).
- Dividing effective exhaust velocities, $I_{sp} g$, by the required velocity, to get $v_{e,1} = I_{sp,1} g / v_t $ as the effective dimensionless velocity for the first stage and $v_{e,2} = I_{sp,2} g / v_t$
Plugging this into the rocket equation gives $$\Delta v_1 = v_{e,1} \ln\left(\frac{1+m_3}{\phi * e_1 + 1 - \phi + m_3}\right) $$
$$\Delta v_2 = v_{e,2} \ln \left( \frac{1-\phi+m_3}{(1-\phi) e_2 + m_3} \right) $$ with $\Delta v = \Delta v_1 + \Delta v_2$. Plugging in the parameters and solving the equation $$\Delta v_1 + \Delta v_2 = 1$$ (iteratively) for $m_3$ will give you the payload for a given rocket mass, which should be maximized.
So I plugged in some values for a Falcon 9:
$$v_t = 9.5 km/s$$
$$I_{sp,1} = 290s$$
$$v_{e,1}=0.305$$
$$v_{e,2}=0.358$$
$$I_{sp,2}=340 s$$
$$e_1=18 t/385 t = 0.0468$$
$$e_2= 4.9t/90t=0.0544$$
After varying $phi$ and also calculating the velocity of the second stage, I got
phi m_3 delta v 2
0.2 0.0160 0.895
0.4 0.0241 0.858
0.6 0.0308 0.753
0.7 0.0331 0.683
0.8 0.0339 0.592
0.9 0.0313 0.456
So, there is a relatively broad optimum where the first stage has around 80% of the mass of the total rocket and the second stage is responsible for around 60% of the total $\Delta v$.
Plug this into the original assumption of a $\Delta v$ of around 9.5 km/s, and you get to the (approximate) 6 km/s for the second stage.
Why doesn't the first stage become faster? Probably because it is the one which has to fight gravity and drag. 180 s at 10 m/s^2 could cost you around 1.8 km/s if you were firing straight up (which nobody is doing, I know...)
Compare this to the actual mass fraction of the first stage of a Falcon 9, which is around 0.809... I probably came out a bit closer than I had a right to expect.