Is ist true that Arithmetic Geometry can roughly be separated into two areas: 1) Showing that motivic $L$functions are automorphic. 2) Calculating special values of these $L$functions.

No, I think your suggested dichotomy misses too many vitally important results in arithmetic geometry. In particular, there are purely Diophantine questions (and answers) which are not informed by any automorphic/motivic considerations whatsoever. As a point of philosophy, you might want to speculate that some of these results will eventually have automorphic interpretations, but in many cases there is not even presently a conjectural relation. To give a specific example, I will go out on a limb and claim that the single greatest theorem in arithmetic geometry is Faltings' proof of the MordellLang Conjecture (informally, I like to think of this as the FaltingsVojtaFaltings theorem): if $A$ is an abelian variety over a number field $k$, and $\Gamma \subset A(\overline{k})$ is a subgroup such that $\dim_{\mathbb{Q}} \Gamma \otimes \mathbb{Q} < \infty$, Then for any closed subvariety $X \subset A$, there exists $n \in \mathbb{Z}^+$, $\gamma_1,\ldots,\gamma_n \in \Gamma$ and abelian subvarieties $B_1,\ldots,B_n$ of $A$ such that $\Gamma \cap X(\mathbb{C}) = \bigcup_{i=1}^n \gamma_i + (B_i(\mathbb{C}) \cap \Gamma)$. In particular, this reduces Faltings' earlier finiteness theorem (finiteness of $k$rational points on a curve $X$ of genus at least $2$) to the MordellWeil theorem and recovers the ManinMumford conjecture (that a curve of genus at least $2$ embedded in its Jacobian contains only finitely many torsion points). Some good articles on the subject include: http://www.math.jussieu.fr/~hindry/abvarmodel.pdf (The last one gives a signficantly more general result!) If anyone can relate this seminal result to motivic/automorphic anything, I would be very interested to know. 


No, because there is the area called Diophantine geometry, and the formulation assumes it can be absorbed into "nonabelian class field theory" and "algebraic Ktheory". We don't know that it can't, if you take the scare quotes broadly enough. But the theory that it can seems to me like one of those mathematical "mergers and acquisitions" deals that appeats good and fashionable on paper, for a while. If however you look at those three just for 30 seconds, you may see the old algebraanalysisgeometry trio staring back at you (automorphic theory for the analysis, the geometric approach to equations being what Diophantine geometry has as its whole rationale). And then you might decide you have seen this one before. 

