I played and liked WotR a lot when it came out years ago and just realized that Battle Realms was made by the same developer, Liquid Entertainment. WotR looks like a Lord of the Rings reskin for Battle Realms.

For anyone that has played both extensively, what are the differences? Is one superior to the other?

i would say that that's more or less what WotR is, a reskin.
in my opinion, Battle Realms is the better game, but WotR is far from bad i'd say.

besides the engine/controls, you will also recognize many voice actors between the games. fortunately, the voice actors are awesome. :-) i've always been particularly fond of the voice actor for Gandalf / Koril. personally i prefer the BR voice acting over that of WotR.

despite using the same engine, gameplay-wise there are a couple of big differences. for one, in BR the factions function very similarly, while in WotR the Evil and Good campaigns play very differently. base defenses work differently, resources work slightly differently (in BR they are infinite).

one similarity is that Heros are strong, and typically have a huge impact on battles. both games share a similar system for special resource points that make heros stronger, or can be used to purchase upgrades or new heros.
and i think in both games, most(all?) units have at least one ability. fun!
great music in both games.

not sure what else to say! i think there's a fair chance that if you like one game, you will probably like the other as well.
i ultimately prefer the gameplay of BR more, but of course that's a subjective thing.
in terms of game-design, i think WotR is not as good.

The shortest (and, I guess, biased) answer is:

Battle Realms is Battle Realms.

WotR is almost a Warcraft copy in the LotR setting.

The armor system, and many other unique aspects that could be seen in BR including the absolutely insane (in a good way) combat mechanics, from BR (6 damage types and armor against them with different multipliers) was dumbed down to RockPaperScissors triangle (don't know about the details though). Generally, WotR feels like Warcraft in general.

Battle Realms, in my opinion, is a much better and a very unique RTS. It is heavily different from WotR too (it is far too different to just call WotR a "reskin" for it). Chances are you might not like it for being complicated and playing differently.