With the current microtype from TeXlive 2011, you can do the following:
\documentclass{article}
\usepackage{fontspec,microtype}
\defaultfontfeatures{Ligatures=TeX, Scale=MatchLowercase}
\setmainfont[SmallCapsFeatures={LetterSpace=6}, Numbers={Proportional,OldStyle}]{Minion Pro}
\setsansfont[LetterSpace=3, Numbers={Proportional,OldStyle}]{Myriad Pro}
\SetProtrusion
[ name = min-eu2 ]
{ encoding = {EU2},
family = MinionPro }
{
{,} = { ,500},
- = { ,500}
}
\begin{document}
\hsize 3in
When, while the lovely valley teems with vapour around me, and the meridian sun strikes the upper surface of the impenetrable
foliage of my trees, and but a few stray gleams steal into the inner sanctuary, I throw myself down among the tall grass by the
trickling stream; and, as I lie close to the earth, a thousand unknown plants are noticed by me.
\end{document}
LuaTeX with fontspec uses EU2 encoding internally, so all you need to do is the regular microtype setup with encoding EU2.
There's a technical and an aesthetical side to most of the questions you're asking:
1.1) For your purposes, a tech report with maths etc.: none of them. You'll have trouble finding math supplements that go well with any of these fonts. Yes, there are packages that set out to provide math symbols supposed to look good with »Garamond«, but the huge number fonts with »Garamond« in their names vary considerably in terms of their look.
A package providing TeX support for a Garamond will most likely be geared towards one of the free Garamond versions, such as URW's (an early digitization of the Stempel version from the 1920s). It may be, but IMHO will rather not be suitable for AGPPro ...which is a highly idiosyncratic rendition of C. Garamond's typefaces.
What I suggest, from a technical/practical perspective is: choose a font that comes with sufficient math support out of the box, or one where you're certain that suitable high-quality math support is available (such as MinionPro).
1.2) The three fonts you list are designed as rather faithful renditions of faces created 500 years ago (unlike e.g. TNR, which doesn't have one specific model). They're explicitly citing the aesthetics of that time -- this is the case with the two (very different) Bembo renditions, and it is even more the case with AGPPro. Both AGPPro and BBook are, in addition, designed to reproduce the look of letterpress printing to some degree.
None of this is a problem per se, but typography is not art for art's sake, but rather halfway between an art and a craft IMHO. So you have to make sure your typeface choice is appropriate within the context of your product. Questions like: »what's the message brought across by a document that tries to look like it's been printed in 1540?«, or »what kind of aesthetics is my audience used to?« are the ones you should consider here.
2) The old (1990s) digital renditions of Bembo were infamous for their thin and anemic look in print. They were horrible digitizations of horrible photo-type-izations of a typeface that was, and remains, sublime in hot metal. These digitizations were shunned by most decent typographers, which I understand perfectly well, having compared books set in Bembo from the three typographic eras side by side.
Now all this was supposed to change with Bembo Book. It was advertised as a font that would bring back the look of that hot metal legend. It didn't. It's about eight (?) years ago IIRC, that MT released BBook, but it still hasn't caught on. Yes, the strokes are sturdier, the thinness is gone, but like its predecessors it lacks any sparkle, and, unsuprisingly, comes nowhere near the original that it's (and has to be) measured by. So that's a strict NO for your Bembo Std, and an if-need-be for Bembo Book, in terms of aesthetics and reading comfort.
AGPPro... one guideline (I'm not saying ›rule‹) is that typography is best when it's invisible. Reading comfort is reduced the more the typography (e.g., the typeface) is making the reader aware of its presence. The more you deviate from what readers are used to, or what just »works«, the more this will be the case. Try setting your text ragged-left (!), for example. For typefaces, the equivalent of a left rag would be choosing a particularly idiosyncratic typeface, i.e. one that draws attention to itself (which is what it all boils down to). Within the range of text faces currently on the market, AGPPro is clearly on the idiosyncratic side of the spectrum (which is why it's hardly being used for serious book production).
The other side of that spectrum we might call »inconspicuous« ones and put, say, TNR or Minion there. The degree of perceived idiosyncracy will of course be dependent on what your readers are used to. Computer Modern will look odd to people from the humanities, but will make maths people feel at home. In Germany, Stempel Garamond (unlike AGPPro) is one of the most inconspicuous choices simply because literally generations have been socialized with it in school, while, conversely, New Century Schoolbook (and classicist or »didone« or »modern« faces in general) look weird to most people over here.
I see I need to keep it more concise:
3) what features do you need? I suggest you consider that question first, and then see what fonts might offer it. At the moment, I'm having trouble understanding the role you have in mind for, say, swashes in a tech report ;)
4) as you're already using LuaLaTeX, you already got the most appropriate tool available in the TeX world. ConTeXt might be another good choice. But choose wisely, as jumping ships between the two might be difficult once your project has taken up speed.
Swashes -- I'm afraid you're trying to do something that, by its very nature, won't work. A swash is usually defined as a calligraphy-style embellishment, mainly for capital letters. The »calligraphy« part is important here, as it's the italic cuts of a typeface that make reference to handwriting. And it is, traditionally, only here that you'll find swashes. So unless AGPPro's specimen sheet says otherwise, there'll be no upright swashes in AGPPro. This, on the other hand, works fine (in LuaLaTeX):
\documentclass{article}
\usepackage{fontspec}
\setmainfont[Contextuals=Swash]{Minion Pro}
\begin{document}
\itshape
Quad Qed Jawohl
\end{document}
Best Answer
It is rather unclear what you actually want. But here two suggestions: You could still use SourceSerifPro as main font and fake a slanted font:
Or you can use SourceSansPro as main font which will work out-of-the-box: