Let $\mathcal{A}$ be a Weyl arrangement. We introduce and study the notion of $\mathcal{A}$-Eulerian polynomial producing an Eulerian-like polynomial for any subarrangement of $\mathcal{A}$. This polynomial together with shift operator describe how the characteristic quasi-polynomial of a new class of arrangements containing ideal subarrangements of $\mathcal{A}$ can be expressed in terms of the Ehrhart quasi-polynomial of the fundamental alcove. The method can also be extended to define two types of deformed Weyl subarrangements containing the families of the extended Shi, Catalan, Linial arrangements and to compute their characteristic quasi-polynomials. We obtain several known results in the literature as specializations, including the formula of the characteristic polynomial of $\mathcal{A}$ via Ehrhart theory due to Athanasiadis (1996), Blass-Sagan (1998), Suter (1998) and Kamiya-Takemura-Terao (2010); and the formula relating the number of coweight lattice points in the fundamental parallelepiped with the Lam-Postnikov Eulerian polynomial due to the third author.