The big issue with this sort of comparison is that fans of BYU know about Holker and are excited about him. Whereas a Utah (or neutral) fan looks and sees a guy who has 19 total catches three years ago and doesn't see what the hype is.
Similarly, if you're a BYU fan, you know all about Kuithe, but don't get why the Utah fan is excited about Fortheringham and Kincaid.
I'm in a somewhat unique position since I follow both teams and want both to be successful. My assessment ends up being basically Kuithe vs Rex with both teams having unproven, but exciting depth. Holker looks great, but Utah also has quality depth. Given that, I have to lean Kuithe given that he's done more (yardage wise, Rex beat him on TDs) over a longer period against better competition with a worse QB throwing him the ball.
That said, I do think BYU's TE room has more upside, given Holker's potential and Rex's age. But based on where they are at the moment, I'd give the slight edge to Utah.