It seems to me that there is a clear, intuitive reason for extending the real number system to the complex number system. Namely, some polynomial equations that have no solutions in $\mathbb{R}$ become soluble in $\mathbb{C}$. When we do this, we lose almost none of the nice algebraic properties of the reals, and pick up some nice new ones along the way (e.g. fundamental theorem of algebra).
However, I cannot see such an intuitive reason for similarly extending $\mathbb{C}$ to $\mathbb{H}$, other than "because we can." In so doing, we actually lose the important property of commutative multiplication. So precisely what problems do we solve by moving from $\mathbb{C}$ to $\mathbb{H}$?
I am of course aware of the quaternions' numerous applications to 3D geometry; what I am really interested in here are the analytic properties they provide. Does quaternionic analysis offer results comparable to those of complex analysis?
I assume that you're referring solely to solving equations (rather than applications of quaternions, like modelling 3D vectors), in which case there is not really much point in extending $\mathbb{C}$ to $\mathbb{H}$; in terms of solving polynomial equations, it's actually superfluous to solve in $\mathbb{H}$. e.g. $w^2=-1$ has two solutions in $\mathbb{C}$, but infinitely many in $\mathbb{H}$. Also, some (non-polynomial) equations cannot be solved in $\mathbb{C},$ but can be solved in $\mathbb{H}$- take, for example, $(xi-ix)^2=-1.$ In $\mathbb{C}$, $xi=ix$, so you get $0=-1$, which clearly has no solution, but in $\mathbb{H},$ using the fact that $xi \neq ix,$ we can, indeed, solve this. So, whilst you imply a lack of commutativity is a bad thing, we see that, in this case, it's necessary in order to solve this equation.
Another example, regarding associativity this time is: $(xi)y-x(iy)=1$. Note that, in $\mathbb{H}$ (and any subsets therof), there are no solutions to this equation; we end up with $0=1,$ which has no solutions. Now, in the octonions, $\mathbb{O}$, this equation does have a solution, since $(xi)y \neq x(iy)$ (due to lack of associativity in the octonions).
So, to conclude, purely with regard to equation solving, extending $\mathbb{C}$ to higher dimensions ($\mathbb{H, O, S, }$ etc.) allows us to solve previously-unsolvable equations (for example, by exploiting a lack of commutativity and/or lack of associativity). It also lets us find even more equations to polynomials (although why anyone would want so many solutions is beyond me).