Numbering cases within cases

My suggestion would be to \tag the respective equations with the necessary numbering scheme. You can use combinations of \theequation, for example, in order to make things consistent with the remainder of the document, and step equation before/after the aligned equations:

\documentclass{article} \usepackage[overload]{empheq} \begin{document} \begin{alignat}{2}[left={S=\empheqlbrace}] & A + B + C & \text{if $a < 1$}, \tag{1.1a} \\ S_1 = \smash{\left\{\renewcommand{\arraystretch}{1.2} \begin{array}{@{}c@{}}\mathstrut\\\mathstrut\\\mathstrut\end{array}\right.\kern-\nulldelimiterspace} & D + 2\bigl( \textstyle\sum_i EF + \nonumber \\ & \quad 2 GH \bigr) + K - L & \text{if $a = 1$}. \tag{1.1b} \\ S_2 = \mathrlap{1} \hphantom{\left\{ \begin{array}{@{}c@{}}\mathstrut\\\mathstrut\end{array}\right.\kern-\nulldelimiterspace}& \tag{1.2} \\ \raisebox{-.6\normalbaselineskip}[0pt][0pt]{$S_3 = \smash{\left\{ \begin{array}{@{}c@{}}\mathstrut\\\mathstrut\end{array}\right.\kern-\nulldelimiterspace}$} & \textstyle\sum_i I + \sum_i J & \text{if $a = 0$} \tag{1.3a} \\ & 0 & \quad\text{otherwise.} \tag{1.3b} \end{alignat} \end{document} 

As an extremely partial answer, I note that subequationsenvironement can be nested with amsmath. Playing with counters allows to obtain the desired numbering. The obvious and important unsolved problem is the outer brace.

\documentclass[12pt, a4paper]{article} \usepackage{amsmath} \begin{document} \begin{subequations} \renewcommand{\theequation}{\theparentequation.\arabic{equation}} \begin{subequations} \renewcommand{\theequation}{\theparentequation.\alph{equation}} \begin{equation} a = b \end{equation} \end{subequations} \begin{subequations} \renewcommand{\theequation}{\theparentequation.\alph{equation}} \begin{equation} a = b \end{equation} \end{subequations} \end{subequations} \end{document}