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.
A number of answers:
Firstly, microtypography is (in my book) the art of enhancing the appearance of a document while exhibiting the minimum degree of visual obtrubsion, that is, ideally, without even being recognisable: Characters with less optical weight should slightly protrude into the margin to make it appear more even, but they shouldn't stick in your face; fonts may be distorted ever-so-slightly to allow for better line breaks, but they should not look distorted. Therefore, it is actually good that you don't see any difference. You should, however, make sure that something does indeed happen: for protrusion, find a hyphen at the end of a line and check whether it protrudes, as it should do, into the margin (by about half of its length), or whether it is fully contained in the text block; for expansion, check whether line breaks in a longer paragraph change when you remove the lines your colleague added. If line breaks are the same in both cases, and if hyphens don't hang over, then protrusion and expansion are in fact not enabled at all, which would be a topic for a new question.
Secondly, the microtypepackage tries to lift the burden of deciding about settings as much as possible from the user. Considering that you say yourself that you are not a man of the finer arts, I would advise to just load the microtype package without any options at all. (In your code, the protrusion and expansion options are superfluous as they are enabled anyway, babel doesn't have any effect, only final may be justified to ensure that line breaks don't change when adding draft as a class option.)
Now for the final point, which obviously causes the most confusion. As Jörg has pointed out, you are using both the microtype package as well as lualatex's own microtypography feature (with the latter taking precedence). You should therefore decide, and either load microtype:
\usepackage[final]{microtype}
\usepackage{fontspec}
\setmainfont[Numbers={OldStyle, Proportional},
Ligatures=TeX
]{Brill}
or use lualatex's techniques:
\usepackage{fontspec}
\protrudechars=2 % or \pdfprotrudechars=2 and
\adjustspacing=2 % \pdfadjustspacing=2 with luatex < v0.85
\newfontfeature{Microtypography}{protrusion=default;expansion=default}
\directlua{fonts.protrusions.setups.default.factor=.5}
\setmainfont[Microtypography,
Numbers={OldStyle, Proportional},
Ligatures=TeX
]{Brill}
I would advise to go with the first, as microtype's settings are more complete and balanced IMHO (but then, I am, of course, biased ...). The second option has the advantage of better integration with luatex. Here, a factor of .5 seems reasonable (the default protrusion, especially of the hyphen, is just too much, quite obtrusive and therefore contradicting the idea of microtypography to me).
Best Answer
I'm currently using Adobe Caslon Pro in my document alongside micro type. These are the settings I have:
These settings look great for me and so far these are the parameters I've been successfully able to tinker with. Be sure to use the beta of micro type (2.5 build8) to prevent any issues with xetex or luatex.
I'm building my documents via LuaLaTeX and I'm using
microtype2.5 beta 8. So far everything works fine.