I don't really consider either one to be above the other. They both have things that I liked but had to be sacrificed for their respective mechanics to work correctly, which is sort of a shame. I think of them as being sides of the same coin, both objectively and in the sense of how much I found their sections fun.
The Twilight Realms did appear tedious at first, but I warmed up to them for the same reason I liked the triforce hunt in WW; because it gave me a reason to wander around, and wandering around is fun. The Silent Realms might have been more, to put it somehow, "active", since you were put in a smaller area and had a proportionally similar number of things to do, but the restriction took off the wandering around part in exchange for more tension and less tedium (your mileage may vary on that, and I'm pretty sure mine does). I did not find wolf Link gameplay to feel different at all from normal Link gameplay beyond the obvious changes, so that part didn't bother me. The huge extensions of land might be tedious, but it made up for it on the visual sense to me. In short, I don't really find the SR's more active concept to be that much of an improvement over the TR's little-tasks-spread-over-large-extentions. I guess it's pretty much a quid pro-duo (read: give and take) situation, but since I'm slightly more fond of wandering around than I am of just coming and doing, I think I liked the TRs somewhat better. SR is still fun, though.
On a different note, I also like the TRs over the SRs from an aesthetic point of view. It goes above the JMEBD rule (also known as: Just Make Everything Brown Dammit) and goes a little bolder with its color scheme, which to me is an added bonus. The Silent Realm, on the other side, was pretty much the JMEBD except with blue, though, the effect when a guardian sees you is pretty cool and helps it a bit. I guess I'm just too fond of wandering overall.
