How to improve the look of a math expression with long superscript?

Some visual adjustments with \, in suitable places, to make more room and help parsing the formulas.

\documentclass[11pt,openright]{book}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\pagenumbering{gobble}
\usepackage{mathtools}
\usepackage{relsize,amsmath}
\usepackage{amssymb}

\begin{document}

\begin{equation}
\mathrm{MRC}^{t}=
  \max\biggl\{
    \mathrm{VaR\,}_{\mathstrut 0.99}^{\mathstrut t-1,10}\, , \;
    \frac{k}{60}\sum_{i=1}^{60}\mathrm{VaR\,}_{\mathstrut 0.99}^{\mathstrut t-i,10}
  \biggr\}
\end{equation}
where MRC is the Market Risk Capital required at time $t$ and 
$\mathrm{VaR}_{\alpha}^{j,h}$ is the day $j$'s Value at Risk calculated
with a holding period of $h$ trading days and an $\alpha$ confidence level

\end{document}

As you see, the adjustments are not necessary in the inline version, where just symbols are used.

I added a thin space before the comma and a thick space after it, besides \mathstrut in the subscripts and superscripts. I also used \biggl and \biggr instead of \left and \right, in order to make the braces less prominent.

I would not mess with their sizes, but (if doing anything) insert more space between subscript and superscript. Also, make sure you don't have an empty line after displayed equations to avoid undesirable indentation.

\documentclass[11pt,openright]{book}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\pagenumbering{gobble}
\usepackage{mathtools}
\usepackage{relsize,amsmath}
\usepackage{amssymb}
\DeclareMathOperator{\VaR}{VaR}
\begin{document}

\begin{equation}
\mathrm{MRC}^{t}=\max\left\{\mathrm{VaR}_{0.99}^{t-1,10}, \, \frac{k}{60}\sum_{i=1}^{60}\mathrm{VaR}_{0.99}^{t-i,10}\right\}
\end{equation}
\begin{equation}
\mathrm{MRC}^{t}=\max\left\{\VaR_{\vphantom{(}0.99}^{\mathstrut  \vphantom{(}t-1,10}, \, \frac{k}{60}\sum_{i=1}^{60}\VaR_{\vphantom{(}0.99}^{\mathstrut \vphantom{(}t-i,10}\right\}
\end{equation}
%
where MRC is the Market Risk Capital required at time $t$ and $\text{VaR}_{\alpha}^{j,h}$ is the day $j$'s Value at Risk calculated
with a holding period of $h$ trading days and an $\alpha$ confidence level

\end{document}.