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H.254 is nothing new - it's a MPEG4 standard. The "new" hype now is that the new update of Flash Player 9 (specifically Player 9 update 3) is able to stream H.254. That said, it requires the newest Flash player. On2 VP6 does not.
Also, currently H.264 can't be embedded into a SWF file which may or may not be an issue for you.
Finally, H.264 requires a license (paid to MPEG-LA), On2 VP 6 does not. Again, may or may not be an issue for you.
Quality wise they are about comparable.
H.264 encoded videos tend to require higher processing power on the user's machine.
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