Xenophon, I'm not seeing this difficulty --- spacing is fine for me w/ Zapfino from a .pdf made using Apple's pdf object and viewed on a PC (using Adobe Acrobat Approval 5.0) --- did you have a specific font, size, and Acrobat implementation which exhibited it? The .pdf of Mike Brotherton's _Star Dragon_ which I made and available from
www.mikebrotherton.com uses ligatures and displays fine on my PRS-505.
Some of the ligatures in Zapfino in the Mac OS X-generated .pdf were messed up when viewed on my PRS-505, but when I switched to a .pdf made by InDesign, they were fine, so the problem would seem to be w/ how TrueType fonts w/ unusual encodings or more than 256 characters are handled by the reader's .pdf implementation (ID converts embeds the font as CID-keyed).
For those who don't have Zapfino, you can see the ligature construction in my TUG2003 paper:
http://www.tug.org/TUGboat/Articles/.../tb77adams.pdf
William