Let's start by considering the uses of multiplication of complex numbers, since that is how you tried to derive an intuition about quaternions being suitable for rotation in $\mathbb R^3.$
First, it might be worth noting that to use complex numbers for rotation, we use multiplication, and that although $\mathbb C$ is in some ways isomorphic to $\mathbb R^2,$ the field of $\mathbb C$ with multiplication is not isomorphic to $\mathbb R^2,$ at least not in the sense that we would have "guessed" the rules for complex multiplication just by looking at obvious operations to perform on $\mathbb R^2.$
See an answer to an earlier question for further discussion.
Now let's consider the function $f(x) = \cos x.$
This is a transformation on $\mathbb R,$ that is,
a function $\mathbb R\to\mathbb R$;
its input and output are strictly one-dimensional.
But we can also write $f(x) = \Re[e^{ix}],$
that is, we can use complex numbers (which are two-dimensional in this context) to express a one-dimensional operation.
This seems to add a lot of unnecessary complexity (pun intended) to something that really only needs one dimension, not two, but electrical engineers and physicists find that this "unnecessary complexity" actually simplifies a lot of calculations.
You could think of rotation by quaternions in a similar way:
as an "unnecessary" extra dimension added to the three-dimensional space of the objects you want to rotate, which happens to be handy for calculation.
We allow intermediate steps of the calculation to have this fourth dimension, but in the end we will be back in three dimensions again.
As for how to make sense of the fact that $i^2 = j^2 = k^2 = -1,$
we need to review some details of how calculations with quaternions relate to rotation in $\mathbb R^2.$
Referring to
an answer to another previous question,
we can write a quaternion in the form
$$ q = w + ix + jy + kz,$$
and define the conjugate of the same quaternion as
$$ q^* = w - ix - jy - kz,$$
that is, the conjugate has the same real part but opposite imaginary parts.
We can also view the imaginary parts of a quaternion as a vector in
$\mathbb R^3,$ so $\mathbb R^3$ is (in this sense) isomorphic to the set of purely imaginary quaternions.
Then if we take a purely imaginary quaternion $r$ and a unit quaternion
$q$ (such that $qq^* = 1$), the product
$$ r' = qrq^* $$
gives the same result $r'$ that we would get if we made the usual identification of $r$ with a vector in $\mathbb R^3$ and
rotated it by an angle $\theta$ around an axis $\hat n = (n_x, n_y, n_z),$
where
$$ q = \cos\frac\theta2 + (in_x + jn_y + kn_z)\sin\frac\theta2. $$
Notice that $q$ can be purely imaginary only if
$\cos\frac\theta2 = 0.$ A purely imaginary quaternion corresponds to a rotation by $\pi$ radians ($180$ degrees).
Perform the same rotation twice, and you come back to where you started.
So it works out nicely that $i^2 = -1,$ because if we perform the "$i$" rotation twice, the result is
$$r' = i^2 r (i^2)^* = (-1)r(-1) = r,$$
as it should be.