documentclass{beamer}
usepackage{booktabs}

begin{document}
  begin{frame}{Example}
    begin{tabular}{ll}
      toprule
        bla & bla \
      midrule
        A & A \
        B & B \
        only<1>{%
          midrule
            C & C \
            D & D \ }
      bottomrule
    end{tabular}

    only<2>{Something else}
  end{frame}

end{document}

documentclass{beamer}
usepackage{booktabs}

begin{document}
  begin{frame}{Example}
    begin{tabular}{ll}
      toprule
        bla & bla \
      midrule
        A & A \
        B & B %
        only<1>{%
          \midrule
          C & C %
        }%
        only<2>%
        {%
        \
        D & D  %
        }%
      \ bottomrule
    end{tabular}
  end{frame}

end{document}

begin{frame}{Example}
 only<1>{begin{tabular}{ll}
    toprule
      bla & bla \
    midrule
      A & A \
      B & B \
        midrule
          C & C \
          D & D \
    bottomrule
    end{tabular}
  }
  only<2->{begin{tabular}{ll}
      toprule
        bla & bla \
      midrule
        A & A \
        B & B \
      bottomrule
    end{tabular}
  }
  only<2>{Something else}
end{frame}

documentclass{beamer}
usepackage{booktabs}


% ------- xalt -------

makeatletter

providecommand@secondofthree[3]{#2}

defxalt<#1>{%
    if *#1%
        % matches any overlay
        expandafter @secondofthree
    else
        % continue overlay check
        expandafter @firstofone
    fi
        {@xalt@checkrange<#1->}%
}

def@xalt@checkrange<#1-#2>{%
    ifx relax#2relax
        % is not a range
        expandafter @firstoftwo
    else
        % is a range
        expandafter @secondoftwo
    fi
        {@xalt@checknumber<#1>}%
        {@xalt@checklower<#1-#2>}%
}

def@xalt@checknumber<#1>{%
    ifnum beamer@slideinframe=#1
        % overlay is matched
        expandafter @firstoftwo
    else
        % overlay is *not* matched
        expandafter @secondoftwo
    fi
}

def@xalt@checklower<#1-#2>{%
    ifx relax#1relax
        % lower bound not given => match
        expandafter @firstofone
    else ifnum beamer@slideinframe<#1
        % overlay is *not* matched
        expandafterexpandafterexpandafter @thirdofthree
    else
        % lower bound is matched
        expandafterexpandafterexpandafter @firstofone
    fi fi
        {@xalt@checkupper<-#2>}%
}

% #2 ends with an additional -

def@xalt@checkupper<-#1->{%
    ifx relax#1relax
        % upper bound not given => match
        expandafter @firstoftwo
    else ifnum beamer@slideinframe>#1
        % overlay is *not* matched
        expandafterexpandafterexpandafter @secondoftwo
    else
        % upper bound is matched
        expandafterexpandafterexpandafter @firstoftwo
    fi fi
}

makeatother


% ------- toprule -------

letoriginaltoprule=toprule

defoverlayawaretoprule<#1>{%
    xalt<#1>%
        {toprule}%
        {addlinespace[dimexpr abovetopsep + heavyrulewidth + belowrulesep relax]}%
}

renewcommand{toprule}[1]{%
    ifx <#1%
        expandafter overlayawaretoprule
    else
        expandafter originaltoprule
    fi
    #1%
}

% ------- midrule -------

letoriginalmidrule=midrule

defoverlayawaremidrule<#1>{%
    xalt<#1>%
        {midrule}%
        {addlinespace[dimexpr aboverulesep + lightrulewidth + belowrulesep relax]}%
}

renewcommand{midrule}[1]{%
    ifx <#1%
        expandafter overlayawaremidrule
    else
        expandafter originalmidrule
    fi
    #1%
}


% ------- bottomrule -------

letoriginalbottomrule=bottomrule

defoverlayawarebottomrule<#1>{%
    xalt<#1>%
        {bottomrule}%
        {addlinespace[dimexpr aboverulesep + heavyrulewidth + belowbottomsep relax]}%
}

renewcommand{bottomrule}[1]{%
    ifx <#1%
        expandafter overlayawarebottomrule
    else
        expandafter originalbottomrule
    fi
    #1%
}


% ------- test document -------

begin{document}

begin{frame}{Example}
    begin{table}
    begin{tabular}{ll}
        toprule
            bla & bla \
        midrule
            A & A \
            B & B \
        midrule<2->
            uncover<2->{C & C} \
            uncover<2->{D & D} \
        bottomrule
    end{tabular}
    end{table}

    uncover<3->{Something else}
end{frame}

end{document}

defxonly<#1>#2{xalt<#1>{#2}{}}

begin{document}

begin{frame}{Example}
    begin{table}
    begin{tabular}{ll}
        toprule
            bla & bla \
        midrule
            A & A \
            B & B \
        xonly<2->{midrule}
            xonly<2->{C & C \}
            xonly<2->{D & D \}
        bottomrule
    end{tabular}
    end{table}

    only<3->{Something else}
end{frame}

end{document}