Punctuation
At this point the reader will not be surprised to hear that punctuation behaviors vary between scripts as well.
Sentence ending
Although the reader’s eye may not register it, good Roman typography adds a small amount of extra space between a full stop and the next word than between other words. A simple difference in Cyrillic is that full stops don’t have any more extra space after them than between words (Kolodin et al, 2000), thus it would be important to be able to disable any additional spacing.
Tibetan (།), Devanagari (।), and Ethiopic (።) all have different symbols for sentence ending, each with differing amount of space before and after the marker. Some Ethiopic languages use a different question mark (፧) than the more standard Roman style.
Some Roman languages (such as Spanish) use an opening and closing mark for questions and exclamations. If a non-Roman script did this, that would need to be implemented as well.
Abbreviated text
Punctuation around abbreviated text can be different. There may be space between abbreviations or there may not (i.e. A.D. Jones or A. D. Jones), and the punctuation will quite likely not be a full stop (Ethiopic: እ/እ instead of እ.እ.) (Yacob, 1999).
There are undoubtedly many other punctuation issues not covered here. Most of these differences in punctuation, such as variations in quotation marks, are fairly straightforward, may already be addressed in smart fonts, and will not take a lot to implement.
References
Kolodin, M.Y., O.V. Eterevksy, O.G. Lapko, I.A. Maknovaya. 2000. “‘Russian style’ with LaTeX and Babel: what does it look like and how does it work,” TUG 2000 Preprints.
Yacob, Daniel. 1999. Notes on Ethiopic Localization. http://abyssiniagateway.net/fidel/l10n/index.uni.html.