The Pentax 645D features the PRIME II imaging processor found in the Pentax K-7. This processor is a little slow for displaying its 40-megapixel images, and instant review can seem a bit slow at times. It's certainly not a deal-breaker, but it does introduce noticeable delays in everyday shooting.
The Nikon D800E features Nikon's latest EXPEED 3 processor, which is a little underpowered for its 36-megapixel images as well. However, slowness is only noticeable when trying to view multiple photos per page in playback mode. Instant review, zooming, and overall performance is excellent - and the faster your card, the better. Tests (performed by other sites) have shown that the D800E's file writing speed (in MB/s) actually outperforms the D3x, making it the fastest Nikon in this respect. Thus, in burst shooting mode, the D800E can take advantage of faster cards and you will get a larger burst buffer with such cards. Tests suggest that a 600x Lexar Professional CF card will let you shoot up to 28 RAW files in burst mode, while a 1000x card will let you shoot up to 31, suggesting a maximum write speed of about 65Mb/s (with consumer-grade cards, you'll get about 17 shots in burst mode). The 645D's writing limit is about 25 Mb/s, meaning that 600x card is the fastest you'll ever need.
The D800E can connect your computer via USB3 - the latest in desktop connectivity.
It's also worth mentioning that the D800E has one annoying quirk: in live view, the screen goes blank whenever data is being written to the card. Hopefully (though doubtfully) this will be addressed via a future firmware update.
In terms of autofocus, in continuous mode, the D800E is able to make measurements much more quickly than the Pentax, and thus it feels more responsive overall.
While the 645D has no live view or video mode, the D800E can shoot full HD video at 30FPS or 720p video at 60FPS, which raw video output available via HDMI. While we didn't find the D800E's video autofocus to be that great, the overall video quality was quite impressive. We won't be performing an in-depth evaluation of the D800E's video as part of this review, however.
All our field tests were done with the cameras mounted on a tripod, and for this application, there was no noticeable difference in responsiveness and autofocus between the two (both were set to center-point AF-S). The 645D takes longer to write to the card and won't let you enter playback mode until all the data has been written, however, while the D800E lets you review your image right away even if instant review is turned off.
The 645D does feels a bit dated in terms of overall performance, but this isn't a show-stopper. However, the fact that the 645D lacks live view is a minor inconvenience and will certainly be a little discouraging for those who want see exactly what they're shooting (the viewfinder doesn't quite offer full coverage). The D800E does very well overall, and Nikon did a pretty good job of tuning the hardware for its 36MP sensor - but it's certainly not built for speed like the D4 or D3s.
In the studio, you'll notice that the 645D takes a bit longer to write data to the card, but general performance should feel about the same. The Nikon doesn't truly shine until you start using it in burst mode and with continuous AF.