I also don't understand, which one should use this angle. If you want to describe physics in non-cartesian coordinates, better use Hamilton's principle of least action, where such issues become much less complicated.
Of course even there you need to calculate time derivatives of the position vector. Let's look at the case of two-dimensional motion in cylinder coordinates. First of all one must realize that also the basis vectors become position dependent. So let's first derive this dependence by using a cartesian basis first. The position vector reads
[tex]\vec{r}=r (\vec{e}_x \cos \varphi + \vec{e}_y \sin \varphi).[/tex]
The basis of the cylinder coordinates [itex](r,\varphi)[/itex] is given by the derivatives with respect to these coordinates (and then normalized). First the non-normalized basis vectors are
[tex]\vec{b}_r=\partial_r \vec{r}=\vec{e}_x \cos \varphi + \vec{e}_y \sin \varphi, \quad \vec{b}_{\varphi}=r (-\vec{e}_x \sin \varphi + \vec{e}_y \cos \varphi).[/tex]
One finds that both vectors are orthogonal to each other. Thus usually one also normalizes the basis vectors, using
[tex]\vec{e}_r=\vec{b}_r=\vec{e}_x \cos \varphi + \vec{e}_y \sin \varphi \quad \vec{e}_{\varphi}=(-\vec{e}_x \sin \varphi + \vec{e}_y \cos \varphi).[/tex]
As you see, the new basis vectors depend on the position, and you have
[tex]\partial_r \vec{e}_r=\partial_r \vec{e}_{\varphi}=0, \quad \partial_{\varphi} \vec{e}_r=\vec{e}_{\varphi}, \quad \partial_{\varphi} \vec{e}_{\varphi}=-\vec{e}_r.[/tex]
Now you can calculate the time derivative of the position vector directly in cylinder coordinates. You have by definition [itex]\vec{r}=r \vec{e}_r[/itex] and thus the velocity is given by
[tex]\dot{\vec{r}}=\frac{\mathrm{d} \vec{r}}{\mathrm{d} t}=\dot{r} \vec{e}_r + r \dot{\vec{e}}_r=\dot{r} \vec{e}_r + r \dot{\varphi} \vec{e}_{\varphi}.[/tex]
In the last step, I've used the chain rule for deriving the basis vector [itex]\vec{e}_r[/itex], using the above given partial derivatives. Of course you can also use the cartesian coordinates to come to the same result.
The second derivative with respect to time, i.e., the acceleration gives
[tex]\vec{a}=\dot{\vec{v}} = \ddot{r} \vec{e}_r + \dot{r} \dot{\vec{e}}_r + \frac{\mathrm{d} (r \dot{\varphi})}{\mathrm{d} t} \vec{e}_\varphi + r \dot{\varphi} \dot{\vec{e}}_{\varphi}.[/tex]
Again using the chain rule you get
[tex]\vec{a}=(\ddot{r} - r \dot{\varphi}^2) \vec{e}_r + (2 \dot{r} \dot{\varphi}+r \ddot{\varphi}) \vec{e}_{\varphi}.[/tex]