I think you are starting to compare apples and oranges.
There are features on each of these machines that put them in different realms IMHO.
The emu is a sample-workstation. It has a sequencer, arpeggiator, quantizing, and has very good timing in both MIDI and SCSI.
The yamaha is a sampler, and if you are controlling it from a sequencer or a workstation...that's dandy. But if not, you might get trapped when it comes time to start laying down tracks.
The other consideration: which one sounds better to you for the style of music you are interested in making.
Oh, and since someone asked...no the emu doesn't support as many file types.
Yamaha: Yamaha A3000,SU-700, EX5 and TX16W, AKAI S1000 and S3000, E-mu, Roland, AIFF and Wave compatible
emu: emu, Roland S-700, Akai S-3K/1K/1100, AIFF and Wave.
Of course, the yamaha is a bit cheaper too.
Can't stress it enough...go listen for yourself.