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To me a couple of differences are paper path/handling for the Epson which I think is a little better than the Canon, and mk/PK ink difference. If you are going to constantly change between MK/PK inks the Canon doesn't require an ink swap which can be important. I think the Canon is a little "bigger" from the ones I"ve seen at trade shows, it appears it is a few inches deeper so will extend out into the room.
Longevity issues are another area which may be different. Epson made some nice improvements to the yellow bringing them closer to HP and Canon. Canon's inks have been great performers in this area, but for some reason no data or information is forthcoming about the new inkset. It's delayed long enough now to perhaps be of some concern, although I think they just decided to not pay Wilhelm to run the tests feeling they didn't make enough changes to cause a problem.
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There is one very big difference in the paper feeding arrangements between the two printers: the Epson has a straight-through pass which allows for printing on very thick media such as posterboard and aluminium plates, whereas the Canon does not. This may or may not be important depending on what media the O/P intends to use.
As for the size of the printers, the Canon will fit through a standard North American door, and it is shorter than the Epson SC-P7000 because the ink tanks are mounted behind rather than on the two sides.
Regarding longevity, of course Wilhelm is not the only game in town - there is Aardenburg. I haven't checked whether Mark McCormick Goodhart has any Canon Pro-1000/2000/4000 samples under test, but worth checking just in case he does. Whatever the reason why Canon has been silent on longevity, I think it's a marketing error on their part, which of course doesn't mean that their longevity is a problem - we just don't know and that in itself is a problem!
Regarding Jasper's questions:
Both printers use pigment inks and the longer they are left unused the more prone they will be to needing cleaning. As neither Canon nor Epson are transparent on this matter, we don't really know which uses more ink for these procedures.
There is no clear winner for B&W. Both can make excellent B&W prints. It depends on how well you prepare them for printing and what media you use.
I don't use HP printers, but from all I've seen and read, it doesn't seem that the age of the technology is much of an issue - people who own them generally think very highly of them in terms of print quality and ease of maintenance, and they have unique profiling features worth looking into. The only concern I would have is about HP's relatively scant presence in this market, though I haven't heard of this being a specific problem in any way.