Why do you drop the charge in the crossover method?
Let's figure out the molecular formula for calcium chloride.

Calcium has a +2 charge. Chloride has a -1 charge. 

So with the crossover rule we get

$$\ce{Ca_{-1}Cl_{+2}}$$

But for molecular formulas a -1 is impossible. The coefficients must be positive integers (usually...). Also have a 1 is superfluous, so it is just $\ce{Ca}$ and not $\ce{Ca_1}$.

Now for the chlorine the + is superfluous, so it is just $\ce{Cl_2}$ and not $\ce{Cl_{+2}}$.

I noted that the coefficients must be positive integers. A case where that is not true is when there is a double salt. Say a mixture of NaCl and KCl. The cations and the anions must balance so the formula can be written as

$$\ce{Na}_x \ce{K}_{1-x}\ce{Cl}$$

thus $(x) + (1-x) = 1$ and the charges balance. 

Frankly I find this whole rule thing much to do about nothing. The net charge must be 0. Calcium has a +2 charge and Chlorine has a -1 charge. So you need two -1 charges to balance the +2 charge. Thus $\ce{CaCl2}$. Note that the coefficients must be the lowest common multiple, so it is $\ce{CaCl2}$ and not $\ce{Ca2Cl4}$ which also has a net 0 charge.

So to me the only difficult part is figuring out the charges on the ions. Once you know that, the rest is easy. Making a special rule just seems to be overkill.