Converting all the claims to a single currency is the only logical approach. Keeping the claims separated leads to a bunch of difficult questions:

- Should the BTC creditors only get money from the remaining BTC pool?

- Assets (servers, offices etc) will be sold for Yen, should this money only be used to pay the Yen creditors?

- Expenses are being used from the Yen pool at the moment. Does this mean Yen creditors would get less money?

And let's not kid ourself: No one thinks about the value of Bitcoin in terms of "amount of BTC". Everyone converts it to dollars using the current exchange rate. It's not like there's a society where "50 BTC = big house", and now that you'll only get back 10 BTC (or whatever the ratio is) you can't buy that house anymore.

You could argue about at what rate/date you should convert the BTC claims to Yen, but the only reason people complain now is that the price happens to be higher. I personally think it would be more fair to lock the price to the exchange rate when MtGox stopped trading.

(Disclaimer: I have a 16k USD claim in MtGox)