This answer is about solving the specific problem, that is, initializing \leftroot and \uproot to different values from the default, leaving intact the possibility of using them for particular cases.
The trick is to notice that amsmath uses the values given as arguments to \leftroot and \uproot to set two count registers, \leftroot@ and \uproot@ which are initialized to zero. This happens in the internal macro called \root. Thus one can do
\usepackage{etoolbox}
\makeatletter
\patchcmd{\root}{\uproot@\z@}{\uproot@3 }{}{}
\patchcmd{\root}{\leftroot@\z@}{\leftroot@-3 }{}{}
\makeatother
and now those initial values will be applied, but saying
\sqrt[\leftroot{1}x]{y}
would give the same result as \sqrt[\leftroot{1}\uproot{3}x]{y} without the patching, which might be useful in particular cases. Similarly, \sqrt[\leftroot{0}\uproot{0}x]{y} would give the same result as the original \sqrt[x]{y}.
As Stefan Lehmke points out in his comment, changing the meaning of \sqrt is not really recommended. However, setting a different default for \leftroot and \uproot could be justified with some document fonts. The important thing is to know how the new \sqrt behaves with respect to \leftroot and \uproot.
Making \leftroot and \uproot adding to the default requires a very extensive patching of \root:
\makeatletter
\def\default@leftroot{-3} % set the default value of leftroot
\def\default@uproot{3} % set the default value of uproot
\renewcommand{\root}{\relaxnext@
\DN@{\ifx\@let@token\uproot\let\next@\nextii@\else
\ifx\@let@token\leftroot\let\next@\nextiii@\else
\let\next@\plainroot@\fi\fi\next@}%
\def\nextii@\uproot##1{\uproot@\numexpr(\default@uproot+##1)\relax\FN@\nextiv@}%
\def\nextiv@{\ifx\@let@token\@sptoken\DN@. {\FN@\nextv@}\else
\DN@.{\FN@\nextv@}\fi\next@.}%
\def\nextv@{\ifx\@let@token\leftroot\let\next@\nextvi@\else
\let\next@\plainroot@\fi\next@}%
\def\nextvi@\leftroot##1{\leftroot@\numexpr(\default@leftroot+##1)\relax\plainroot@}%
\def\nextiii@\leftroot##1{\leftroot@\numexpr(\default@leftroot+##1)\relax\FN@\nextvii@}%
\def\nextvii@{\ifx\@let@token\@sptoken
\DN@. {\FN@\nextviii@}\else
\DN@.{\FN@\nextviii@}\fi\next@.}%
\def\nextviii@{\ifx\@let@token\uproot\let\next@\nextix@\else
\let\next@\plainroot@\fi\next@}%
\def\nextix@\uproot##1{\uproot@\numexpr(\default@uproot+##1)\relax\plainroot@}%
\bgroup\uproot@\default@uproot \leftroot@\default@leftroot\relax \FN@\next@}
\makeatother
(Thanks to Stefan Lehmke for spotting an error in the initial version.)
\renewcommandwhich handles optional arguments for you:\renewcommand\sqrt[1][]{\oldsqrt[\leftroot{-3}\uproot{3}#1]}. – Caramdir Mar 23 '12 at 01:34