On Kobo, I prefer KEPUB, mainly because Kobo's EPUB support is lackluster.
I like to read on breaks at work and it is helpful to know if the next chapter has 15 pages or 75. On my old Nook, that was no problem, but on Kobo if you want that sort of advanced functionality

you need to use KEPUB*
The large header and footer can be done away with by implementing full screen reading. The fact that this has to be a patch that is applied rather than an officially supported option makes Kobo look bad (in my opinion).
I do wonder why they don't just add KEPUB features to EPUB. At any rate, since I sideload all my bookings and Calibre makes it a snap to convert an EPUB on my PC to a KEPUB on my Kobo, I just let it go.
*I'm assuming that is still the case. If it has been updated in current releases of the firmware, I am unaware of it.