Alignment using "\lesssim" command
You can lower the symbol by the excess height with respect to <
. But you shouldn't.
\documentclass{article}
\usepackage{amsmath,amssymb}
\let\originallesssim\lesssim
\let\originalgtrsim\gtrsim
\DeclareRobustCommand{\lesssim}{%
\mathrel{\mathpalette\lowersim\originallesssim}%
}
\DeclareRobustCommand{\gtrsim}{%
\mathrel{\mathpalette\lowersim\originalgtrsim}%
}
\makeatletter
\newcommand{\lowersim}[2]{%
\sbox\z@{$#1<$}%
\raisebox{-\dimexpr\height-\ht\z@}{$\m@th#1#2$}%
}
\makeatother
\begin{document}
$A<B\lesssim C\gtrsim D$
$\scriptstyle A<B\lesssim C\gtrsim D$
\end{document}