As usual, these problems can be easily solved thanks to the style visible on defined by Daniel (see Mindmap tikzpicture in beamer (reveal step by step)).
Moreover, it works without problems with custom environments. Demonstration:
\documentclass{beamer}
\usepackage{lmodern}
\usepackage{tikz}
\tikzset{
invisible/.style={opacity=0,text opacity=0},
visible on/.style={alt={#1{}{invisible}}},
alt/.code args={<#1>#2#3}{%
\alt<#1>{\pgfkeysalso{#2}}{\pgfkeysalso{#3}} % \pgfkeysalso doesn't change the path
},
}
\newenvironment{mytikz}[1][]{\begin{tikzpicture}[#1]}{\end{tikzpicture}}
\begin{document}
\begin{frame}
\begin{tikzpicture}[visible on=<2->]
\node at (0,0) (a) {only visible on slide 2};
\node at (2,2) (b) {also only visible on slide 2};
\end{tikzpicture}
Some text here:
\begin{itemize}
\item one
\item two
\end{itemize}
\begin{center}
\begin{mytikz}[visible on=<3>]
\draw[top color=orange,bottom color=magenta!80!purple]
(0,0) rectangle(2,1);
\draw[top color=magenta!80!purple,bottom color=green,radius=0.5]
(4,0.5) circle ;
\end{mytikz}
\end{center}
\end{frame}
\end{document}
The result:

\only<2>in the definition of your new environment, unless you have a more specific example in mind that doesn't work with this strategy. – Herr K. Nov 25 '13 at 22:33