Using Palettes -> Writing Assistant -> Math Cells, you can enter aligned equations such as:
Cell[TextData[Cell[BoxData[
FormBox[GridBox[{
{GridBox[{
{
RowBox[{
RowBox[{"f", "(", "x", ")"}], "=",
RowBox[{"expr", " ", "1"}]}]},
{
RowBox[{"=",
RowBox[{"expr", " ", "2"}]}]},
{
RowBox[{"=",
RowBox[{"expr", " ", "3"}]}]}
},
GridBoxAlignment->{"Columns" -> {{"="}}}]}
},
GridBoxItemSize->{"Columns" -> {{
Scaled[0.96]}}}], TraditionalForm]]]], "Text"]
But saving as $\LaTeX$ yields equations that are unaligned and uncentered!

I'm looking for a SaveAsLatex function that would correctly export human readable code for the following things:
- (marker) Aligned Equations
- Hyperlinks (refs, labels, etc...)
- ItemNumbered cells
- Centered math cells
- Numbered and captioned tables/figures
Here is a sample notebook to test your code.