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In the future, everyone will have the new decoders. So what makes the most sense would be whichever one is the most compact, so that more other data can be fit on the disc as needed. Otherwise, there is no point in either, and the discs may as well just have uncompressed PCM. Probably, if I were running a studio, I would put everything out with uncompressed PCM and not pay for either Dolby or dts. They are not really needed anymore.
Pyrrho, uncompressed PCM wastes a LOT of space. For a BD-50 with minimal extras that's no big deal. However, for a BD-25, space is at a premium, so Dolby TrueHD and DTS-HD MA (or their high res lossless counterparts, DD+ and DTS-HD HR) would be preferable.
I prefer Dolby TrueHD not just since more players support it but for DRC/night mode. Yes, higher end receivers and processors will implement DRC on anything. But most players and receivers will only implement DRC on the Dolby formats. For regular movie watching, I don't do DRC. However, when watching a movie at night while my wife's asleep, it's very preferable.