New options and loaded class options bug?

In order to do this correctly you should create an if-switch or boolean which is modified by the oneside and twoside options of your package, which then pass the final option to memoir. Note that you should process or execute your options before loading another class or package.

\NeedsTeXFormat{LaTeX2e}[1999/12/01]
\ProvidesClass{mythesis}[01/01/2011, v1.0, my own thesis class]
\RequirePackage{ifthen}
\RequirePackage{calc}
\AtEndOfClass{\RequirePackage{microtype}}
%
\newboolean{@myopti}
\setboolean{@myopti}{false}
\newboolean{@myoptii}
\setboolean{@myoptii}{false}
\newboolean{@myopt@oneside}
\setboolean{@myopt@oneside}{true}
%
\DeclareOption{myopti}{\setboolean{@myopti}{true}}
\DeclareOption{myoptii}{\setboolean{@myoptii}{true}}

\DeclareOption{oneside}{\setboolean{@myopt@oneside}{true}}
\DeclareOption{twoside}{\setboolean{@myopt@oneside}{false}}
%
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{memoir}}
\ExecuteOptions{myopti}
\ProcessOptions*
\ifthenelse{\boolean{@myopt@oneside}}
    {\PassOptionsToClass{oneside}{memoir}}
    {\PassOptionsToClass{twoside}{memoir}}
\LoadClass[12pt,final]{memoir}