The main issues are:
The maximum principle fails for higher order elliptic equations.
Somewhat by extension, the De Giorgi-Nash-Moser theory also fails.
The failure of the maximum principle can already be shown using simple examples for the biharmonic equation ($\Delta^2 u = 0$). At a technical level one also sees the proof breaks down since you cannot classify a critical point $x_0$ that satisfies $D^4u(x_0)=0$. This breaks a lot of techniques that work for the (scalar) second order case, including viscosity methods which relies on the concept of subsolutions.
A counterexample of the failure of regularity is due to Maz'ya from 1968, and similar counterexamples for elliptic systems were found by De Giorgi around the same time. At a technical level, one can't use test functions of the type $\max\{0,u-k\}$ for $k \in \mathbb R$ that typically feature in the proofs.
Despite the above difficulties however, some aspects of the regularity theory do still apply to general elliptic equations. For instance:
The difference-quotient methods that work in the $H^k$ spaces, found e.g. in Evans' text or Section 8.3 of Gilbarg & Trudinger readily generalise to the higher order setting.
Linear estimates in the Hölder scales (Schauder estimates, Ch. 6 of G&T) and Lebesgue scales (Calderón-Zygmund estimates, Ch. 9 of G&T) also hold for higher order equations. However, the potential methods used in Gilbarg & Trudinger aren't so easy to generalise, as one needs to construct more complicated kernels. While this can be done, there are other approaches like the approach using Morrey-Campanato spaces to prove Schauder estimates, which can be found in Chapter 3 of Han & Lin.
For quasilinear equations of higher order, pertubative methods can be used to obtain partial regularity; namely that the solution $u$ is smooth away from a "small" singular set $\Sigma \subset \Omega$.
These are usually studied in the context of elliptic systems; the case of higher order equations is usually analogous (I think a formal reduction is also possible in some cases). Here a classic reference is:
Giaquinta, Mariano, Multiple integrals in the calculus of variations and nonlinear elliptic systems, Annals of Mathematics Studies, 105. Princeton, New Jersey: Princeton University Press. VII, 296; 21.50 (1983). ZBL0516.49003.