$$\cos(\theta) = \sin \left(\tfrac{\pi}{2} - \theta\right)$$ $$\sin(\theta) = \cos \left(\tfrac{\pi}{2} - \theta\right)$$
Both are the same entity. But is sine the copy of cosine, or is cosine the copy of sine?
If you really don't see any difference between these two functions, my question could be rephrased as such:
If for the rest of your life you had to only use one of the two following pairs of functions:
$\cos(\theta)$ and $\cos \left(\frac{\pi}{2} - \theta\right)$
$\sin(\theta)$ and $\sin \left(\frac{\pi}{2} - \theta\right)$
...which pair would you choose?
The cosine is nicer because it corresponds to the real part of the exponential of imaginary numbers and its power series is invertible.
The sine is nicer because it is an increasing function for angles in the first quadrant.
For substitution purposes in integrals, you should not neglect the option of choosing $\tan \frac{\theta}2$ as basic.