• oldstyle figures for page numbers and labels
• chapter entries in spaced, lowercase smallcaps
• numbers close (en-space) to the entries, no dotfill

You should be able to see in the MWE that oldstyle figures are produced for all labels and the page-numbers of the sections, but not for the page numbers of the chapters.

The oldstyle figures appear, if I comment either the

• lsstyle command or the
• \usetocstyle{nopagecolumn}

Both indicated in the MWE. As shown in the MWE-chapter Introduction, the combination (lsstyle, scshape, lowercase) works in normal text and produces oldstyle figures.

• there are some problems when setting letterspaced smallcaps with LuaLaTeX. This is why I use the setting \addfontfeature{Renderer=Basic}.)
• you need Microtype2.5 to reproduce the problem
• the problem may be related to this tex.SE entry

MWE

% !TEX TS-program = LuaLaTeX
\documentclass{scrreprt}

\usepackage[english]{babel}
\usepackage[utf8]{inputenc}

\usepackage[letterspace=70]{microtype}

\usepackage{fontspec}
\setmainfont[Numbers={Proportional,OldStyle}]{Minion Pro}

\usepackage{tocstyle}
\usetocstyle{nopagecolumn} % comment this to see OSF
\lsstyle % comment this to see OSF
\lowercase}

\begin{document}
\tableofcontents
\chapter{Introduction}

% to show that the combination works in normal text

\chapter{Methods}
\section{Method A}
\section{Method B}
\chapter{Conclusion}
\end{document}

-
If I add \settocfeature[toc][0]{pagenumberhook}{} all page numbers are oldstyle. –  egreg Mar 3 '13 at 20:14
The empty argument was the trick. I already tried \normalfont and \addfontfeature{Numbers={Proportional,OldStyle}} as pagenumberhook. Still a very weird problem, isn't it? Can you comment why this solution works? –  NauC Mar 3 '13 at 20:26
Sorry, but I tried once to understand tocstyle and gave up. –  egreg Mar 3 '13 at 20:28
Maybe it is a bug, I don’t know, but the package itself prints out a warning on every run, that it is in alpha state. –  Speravir Mar 3 '13 at 21:11