I compare these two because both came out around relatively the same time from two biggests artists of the same label.
Personally I would give Yeezus 3/5 and Magna Carta 4/5.
Yeezus was much more creative in production, but aside from a few hot lines the lyrics were mostly mediocre, which is enough to make the album mediocre.
Magna Carta may not live up to the prestige of Jay's other albums, but in the end, I think it's a quality release that's an excellent adaptation to modern standards without becoming something he isn't. At first, I found myself underwhelmed by his lyrics, but after listening a few times, I got a better understanding of their depth and intellect.