I could be unfairly judging InDesign myself--since I'm mainly comparing my fussy work in XeLaTeX with others' work with InDesign.
Unfortunately, even though I'm the author of the piece in question, I cannot legally distribute the officially published version made in InDesign. The version I made with XeLaTeX is
here. If you'd like to see their version, send me an IM with your email address and I'll send it to you to compare.
I should be clear, however, that there are a lot of improvements I could make to that, and it looks the way it does mainly because I was emulating the journal's style. It's too cramped for my taste, but I was trying to match their pagination and fonts and line height exactly. Bembo and Frutiger also seem like a funny combination, but it's theirs, not mine. I despise end-notes, especially super-cramped ones like this, but again, I was just trying to match their output.
The improvements mainly involve the mathematical/logical formulas. They claimed it was impossible, for example, to have smooth breathing (spiritus lenis) accents rather than acute accents on the Greek vowels, put different spacing around operators as around connectives (or at least they didn't know how).
But there are traditional things mine did better on too. Mine has an ff-ligature. Theirs didn't. Overall, I think mine had more consistent white-space usage than theirs did. I think the kerning overall on mine was better.
This isn't really a great example of the best use of open type fonts in XeLaTeX. For that, see the
Beauty of TeX page or the
fontspec documentation.
I mainly just like the fact that mine was done with free software, and theirs with super expensive software.
I'm not really telling anyone else what to use -- if you're already familiar with, and have access, to InDesign, that's great. It's not as if you're reverting to Word or something atrocious like that.