Uru is probably the best of all the post-Riven games, but if I had to order them, I'd say V>III>IV.
None of them are really bad, but something about Revelation never quite sit right with me. I thought Achenar's redemption was an interesting touch, but I found the actual endgame somewhat lacking - rather like having Indiana Jones enter Atlantis only to find out it's a massive Candy Land board, complete with all the characters thereof; with two incredibly difficult RPG boss fights (on the order of SMT's Demi-Fiend and FFXII's Yiazmat) at the midpoint and end.
Exile was probably more thematically consistent with the rest of the Myst series (even if it felt like they picked up a dictionary and chose names at random - I mean, seriously, "Saavedro" and "Narayan"?), but it felt more contrived overall. It's got spectacle, sure, but it feels as if you're being led through what amounts to a theme park - and I don't just mean the Amateria age (which was, admittedly, awesome at the end).
As for End of Ages? It felt more like a proper continuation - even if it did pick up Uru's story and hence some of its incongruous mysticism. I thought that the best bit was at the end, finally concluding that Yeesha was not the Messiah figure she'd been played up as, and that in a nod to the original game, where you are given a choice of people to trust, you instead take the third, hidden option - to trust neither and find the truth hidden right in front of your eyes.