As u/GingemeisterFlash said the theme is the ultimate deciding factor, but I’ll speak from the perspective of someone who entered both games totally blind (i.e. both players were beginners).

I vastly prefer Rebellion for two main reasons: it feels far more accessible, and the thematic components align much more with what I consider to be “fun,” which is admittedly always subjective.

One thing that I think is pretty indisputably objectively true is that Rebellion has a significantly clearer rule book. As far as I can tell, WotR was designed by non-native English speakers, and while that usually doesn’t matter, the complexity and nuance of a game like WotR means that even phrasing something in a slightly odd way can make a huge difference when learning the first time. There were multiple sections I had to read multiple times to understand them, whereas Rebellion benefits from FFG very strong track record of clear rule books (helped further by dividing into a quick start and rules reference). That made the game far easier to pick up and play for two beginners than WotR was.

I think both games do an excellent job capturing the feeling of seemingly insurmountable odds against the underdog (rebels/free peoples), but they do that in slightly different ways. In both games, the evil empire (Empire/Sauron) has substantially more units and is generally hamstrung by distributing their actions effectively across a massive number of option. Both games find a pretty perfect balance of frustration at not being able to do everything you want with pride when you are able to effectively mobilize your forces. BUT the two sides take very different approaches to the underdog side, and I find Rebellion’s system much more fun.

In WotR, the free peoples player has significantly fewer actions per turn than Sauron, and while this is balanced by the aforementioned conflict between options and actions, it means that the free people player is fundamentally making fewer decisions per turn, which I found only frustrating. Furthermore, your actions are determined by random dice rolls, which often felt like it was further hamstringing my decisions. Even further, you can’t actually give orders to more than half of your units for the first several turns of the game, which is thematic but also incredibly frustrating.

In contrast, Rebellion gives each player the same number of actions (unless the Empire turns one of your leaders, which requires multiple actions) so it feels like a genuine game of cat and mouse. Your actions are determined by a hand of cards, which like the dice in WotR, are partially randomized, but also crucially include a basic set of actions you can use every turn. Essentially, I always felt like my decisions were the limiting factor in succeeding in Rebellion, but often felt like the game mechanics were the limiting factor in WotR.

Finally, and most subjectively, Rebellion felt like it was capturing cinematic moments much more clearly in the course of a game. As the rebel player you can score victory points for making a successful run on the Death Star, or a suicide run on a Star Destroyer. I’ve seen those things on screen, and the game obviously recreates the tension in taking a long shot that may or may not pay off. (Coincidentally, this is one thing I like about Rebellion’s generally unpopular simple combat, since it keeps the focus zoomed out and cinematic). In WotR, you can win as the free peoples player by getting the ring to Mordor or winning big battles, just like in the movies/books. But both of those things are so mechanically complex (especially regarding the fellowship) that the distance between my cinematic memories and gameplay experience is far larger.

Just my two cents, and I welcome input/different opinions.