\begin{filecontents}{aaa.cls}
\RequirePackage{expl3,l3keys2e}
\ProvidesExplClass{aaa}{2014/01/18}{0.1}{Class for typesetting CTU theses and alike}
\keys_define:nn { aaa } {
mykey .code:n = \def\bbb{#1},
myotherkey .code:n = \def\bbbccc{#1},
}
\keys_set:nV { aaa } \classoptions
\LoadClass{article}
\end{filecontents}
\let\origdocumentclass\documentclass
\def\documentclass[#1]{\def\classoptions{#1}\origdocumentclass[#1]}
\documentclass[ mykey = {foo, bar}, myotherkey = baz ]{aaa}
\begin{document}