Let $\mathbb{H}$ be the skew-field of quaternions. I'm aware of the
Theorem 1. A function $f:\mathbb{H}\to\mathbb{H}$ which is $\mathbb{H}$-differentiable on the left (i.e. the usual limit $h^{-1}\cdot (f(x+h)-f(x))$, for $h\to 0$, exists for every $x\in \mathbb{H}$) is a quaternionic affine function on the right (i.e. of the form $x\mapsto x\cdot \alpha + v$).
This means that there are no interesting smooth quaternionic funcions, hence no interesting "quaternionic-smooth manifolds" (which is not the same as the quaternionic-Kahler or hyperkahler structures you encounter in differential geometry and complex analytic geometry).
I think I can also recall the
Theorem 2. If a function $f:\mathbb{H}\to\mathbb{H}$ is locally $\mathbb{H}$-analytic (i.e. it can be locally developped in power series, for the suitable noncommutative notion of "power series"), than it corresponds to a real-analytic function $f:\mathbb{R}^4\to \mathbb{R}^4$, and any real-analytic funcion $f:\mathbb{R}^4\to \mathbb{R}^4$ can be obtained in this way.
That says that $\mathbb{H}$-analytic functions are essentially the same as quadruples of real-analytic functions of 4 variables. Hence there is no "quaternionic-analytic geometry" distinguishable from $4n$-dimentional real-analytic geometry. I think the same happens with quaternionic (noncommutative) polynomials: they're just 4-tuples of real polynomials in 4 variables.
But, is it reasonable that the zero locus on $\mathbb{H}^n$ of a "noncommutative polynomial" with $\mathbb{H}$-coefficients doesn't have any further mathematical structure than it's real-algebraic variety structure? It would be nice to be able to see things such as $\mathbb{HP}^1$ as a "quaternionic curve ", and to speak of a point " $\mathrm{Spec}(\mathbb{H})$ " (whatever it means) if it possible...
Is there a theory of "quaternionic algebraic geometry", maybe as a branch or particular case of some noncommutative (algebraic) geometry theory?
Of course, if such a theory has some sense, it cannot be the "obvious analog" of complex algebraic or analytic geometry, as theorems 1. and 2. above show.