Emilie.Jung said:
what is the difference between the first and the second metric,
First we have to get clear about what these two metrics are supposed to be describing, and what "changing" from one to the other means.
You haven't given a reference for where you got these metrics from (if you have one, it would be helpful to give it), so I'm not sure what physical situation you are thinking about. In general, it's not always possible to just set ##R_2(r) = R_3(r)##; it's only possible in particular cases. Nor is it always possible in general to even write the metric in the first form.
One case in which it is possible to write the metric in the first form is a spherically symmetric spacetime. A general spherically symmetric spacetime only requires two functions in the metric, so in general we can write it in either of two forms. One is the first form you wrote, but with ##R_3(r) = 1##; in other words,
$$
ds^2 = - R_1(r) dt^2 + R_2(r) dr^2 + r^2 d\Omega^2
$$
where I have used ##d\Omega^2## for the angular part of the metric for brevity. The other form, which I will write using ##\bar{r}## for the radial coordinate and ##F_1## and ##F_2## for the functions to make it clear that they are different from ##R_1## and ##R_2##, is your second form:
$$
ds^2 = - F_1(\bar{r}) dt^2 + F_2(\bar{r}) \left( d \bar{r}^2 + \bar{r}^2 d\Omega^2 \right)
$$
The key thing to understand is that these two different formulas are supposed to describe the
same spacetime, i.e., the same geometry. Each surface of constant time ##t## in this spacetime is an infinite set of 2-spheres, each labeled with a radial coordinate (##r## or ##\bar{r}##). The difference in the two forms of the metric is in how the radial coordinate labeling is chosen, i.e., what label is attached to a given 2-sphere.
To see the difference, we need to find some invariant that identifies each 2-sphere. Since the spacetime is spherically symmetric, the area ##A## of a given 2-sphere will be such an invariant. So a given 2-sphere with area ##A## will have two different radial coordinate labels, one assigned by the first metric (##r##) and one assigned by the second (##\bar{r}##).
From the first metric, we can see that ##r## is simply the "areal radius" of the sphere, i.e., ##r = \sqrt{A / 4 \pi}##, so ##A = 4 \pi r^2##. (The way we see this is by looking at the coefficient of the angular part of the metric; the area of the 2-sphere will be the integral of the angular part of the metric over the full range of ##\theta## and ##\phi##, which gives a factor of ##4 \pi## times the coefficient.)
From the second metric, however, we can see that ##A = 4 \pi \bar{r}^2 F_2(\bar{r})##, which means that ##\bar{r} \sqrt{F_2(\bar{r})} = \sqrt{A / 4 \pi}##, so the same 2-sphere of area ##A## will have a label ##\bar{r}## in this metric that is different from its label ##r## in the other metric. We can't know specifically what ##\bar{r}## is in terms of ##A## unless we know ##F_2(\bar{r})##. (To know ##F_2##, we would have to know more about the specific physical situation.)
Emilie.Jung said:
We know that isotropy means no preferred direction
As a matter of physics, yes, but that is not true in general of a spherically symmetric spacetime; the radial direction in such a spacetime is different from the tangential directions. Think, for example, of the spacetime surrounding a gravitating body like the Earth. Obviously things work differently in the radial direction than in the tangential directions; objects fall radially but not tangentially.
As a matter of coordinate choice, however, "isotropy" doesn't mean the spacetime itself has no preferred direction; it just means the coordinates don't. (More precisely, they don't have a preferred spatial direction locally; we'll see what that means in a moment.) The second form of the metric above clearly has this property: the function ##F_2(\bar{r})## multiplies the entire spatial part of the metric, so locally, the radial coordinate ##\bar{r}## doesn't work any differently from the other coordinates. We could underscore this by switching, locally, to Cartesian coordinates; we have ##dx^2 + dy^2 + dz^2 = d\bar{r}^2 + \bar{r}^2 d\Omega^2## (this is just the usual transformation between Cartesian and spherical polar coordinates), and clearly the ##x##, ##y##, and ##z## coordinates all work the same, with none of them picking out a preferred direction.
By contrast, the first form of the metric does not have this local isotropy property in the coordinates; we can't do the same transform to Cartesian coordinates locally with this form of the metric, because the function ##R_2(r)## only multiplies the ##dr^2## term. So even locally, the radial coordinate ##r## in this form of the metric works differently from the others.
But globally, this spacetime clearly does have a preferred direction, the radial direction; we can see that because the metric coefficients are functions of the radial coordinate but not the other coordinates. So as we move radially, from one 2-sphere to another, the geometry changes. That is true for both forms of the metric.