Regarding which subtitles to drop, here's my advice:

Drop the matching subs. I'll admit it--it's a gimmick, just use the regular English subs. But in answer to your question, the v2 subs match the whole v2.x series, including 2.5.

Drop dialects. Drop Castilian Spanish (keeping American Spanish), drop European Portuguese (keeping Brazilian Portuguese), and drop Malay (keeping Indonesian). I'd also say for combined quality/language overlap reasons you could drop Ukrainian.

Keep in mind that by including a dub (i.e. the Thai dub), you'll also need to include the forced subs that go with it. Did I mention we have some dub updates too? ;)

For the rest, just follow the order listed in the Project Threepio README, which roughly follows number of speakers. Get as far down the list as you can and cut the rest. Yes, that will mean you will cut high-quality awesome subtitles like our Icelandic subtitles, and it kinda pains me to see that, but the cut has to be somewhere, and that seems a reasonable way to do it.

Also, when you get ready for a final run, PM me for a more current link. There are some minor fixes that the most recent version doesn't have, and I'd like the Blu-ray to have them.