Before the Berlin 2011 hackathon i published in several Hebrew Wikipedia-related forums a call for the most annoying RTL issues. This was the most frequent complaint:
Parser tags such as <ref>, <poem>, <timeline> etc. cannot be localized. This is not a terrible issue for left-to-right languages, but it is a serious one for RTL languages. For example, <ref> is very often used with URLs, and these get jumbled up. It's hard to write them in the first place, and it's even harder to correct them after they are written. Replacing <ref> with something like <הערה> would make adding references to RTL wikis a lot easier. The same is true for the other tags of this kind.
I talked to Victor Vasiliev and Tim Starling about it in the Berlin Hackathon 2011 and they said that it's generally doable.