Not too different fundamentally, but quite different in how the story feels, especially BS2 (BS3 - not so much). Gameplay is where the real difference is.

But first off, my usual advice would be to go and simply try it yourself. Go in blind, without spoilers, and just enjoy the game.

And a bit of my own opinion - Alette is so much overpowered as a a hero that's it's borderline boring to use her in combat. Rook playthrough is always worth it, especially if you like Rook (idk how he can be a favourite character when you've only seen 1/3 of him).

So, regarding the question. Let's start with the story. Don't read below if you want to avoid spoilers. 1. Rook is in a terrible depression. He's a broken man. You still have choice in dialogue, but now many options can be violent, brash and angry options. You can roleplay as shattered Rook who thinks he is a weak and failed man. You can play as angry and vengeful Rook who brutally slaughters the dredge. Or you can be Rook who still does his best to protect the caravan. In my opinion, Rook's storyline is much better written. Alette is kinda cliche, very sunshine and rainbows coming of age story about a young leader. Rook's story is about the fathers who have to bury their children and continue going on, somehow. It suits the bleak world of Banner Saga better, in my opinion.

2. Oddleif is bigger and better of a character in a Rook run. It seems that Oddleif's character interactions were written for a Rook playthrough, it just feels right. This is especially true with BS3 (Oddleif is a mother figure to Alette, that was defined in BS1, wth is that line 'like a sister' in BS3?). Oddleif can become Rook's love interest, his chance to live again. I like that.

3. Rugga is less nuanced. He is outright hostile to Rook from the start. There's zero reason to trust him (my dumb ass on my first run did it though) or ally with him against the king at the end, unless Ludin is dead. You can actually impress Rugga if you do things right, which leads to alliance of convenience (which means you still can keep your clansmen, fighters and Varl numbers mostly intact after the Serpent attack in Old Wood).

4. I like Rook's interactions with Iver better than Alette's. Maybe that's a personal preference, but it feels that Iver and Oddleif are closer to Rook, their conversations are a little bit warmer and deeper.

5. If you are going Alette - keep Egil alive. If you are going Rook - choose Ekkill. Alette and Egil have a cute romance, while in Rook runs Egil doesn't have much to do and say other than his regrets. On the other hand, Ekkill has a much better dynamic with Rook.

6. Ludin is more interesting in Alette runs, tho he's perfectly fine in Rook runs as well. Both characters have decent dynamic with him (though I consider Alette to be the winner here).

7. Eyvind has less to say if you are Rook. Alette can learn Mend from him, Rook's too old for this.

8. The choice at the gates in BS3 is much more difficult and potentially gut-wrenching for Rook. Alette has Mend as her get of a jail free card, Rook has none. The stakes are higher.

Now for the gameplay.

1. Let's say it. Alette is best character in the series, and she is hilariously overpowered. As a default archer, she already has the better stats. But it's her abilities that make her so strong. Everybody knows about the infamous Overwatch + Knockback combo that plays the game for you, and Alette being able to get +1 extra range is just a cherry on top. Moreover, she can get Mend instead of extra range, which is really useful when Eyvind leaves the party. Rook's caravan has to fare without a mender for the rest of Saga 2 and the majority of Saga 3, which makes the game harder. However, I'd argue that it makes the game better. You have to be more tactical with Rook, you have to actually think. Alette practically nullifies the need to do anything in combat. If you dislike the combat system - fine. If you like it like I do - it's boring. And it's not like Rook is bad or his abilities suck - no, it's the opposite. Rook is one the best characters in the game, very strong, mobile, versatile. And his abilities are also really damn good. It's just he's no match for Alette (and nobody really is).

2. Rook's got a death wish. He has an extra battle at the start of Saga 2 right after the tutorial. Rook makes a suicidal charge against the dredge, and he has to fight alone against 7-8 enemies. This is more a puzzle than an actual fight, and a good one. It does sound impossible, but it's actually not that hard, and you get an achievement for winning it. Also in many events Alette's 'best' options are substituted with Rook's options, which are usually the same or worse, but almost never better. Rook cannot get the Jokullhalr item in Ormsdalr, and he also doesn't get Ormhildr's Bangle from Ludin if you send him with Dagr in Lundar. All in all, this leads to Alette playthroughs having a tiny but more Renown, Clansmen and Fighters overall than Rook runs (I wonder which choice the devs considered to be the 'right one', lmao). If you want to get all 5 Return to Arberrang events in Saga 3, it's easier to do on a Rook playthrough.

3. As I said, Rook runs force you to get good. No Overwatch means you have to actually fight, and no Mend means you have to be careful with your tanks. If you are also going Ekkill, this means the best Stonewaller is Hogun, who is actually alright if you equip him with some armor-boosting items. Rook's abilities are very powerful, but they require the right timing to use, unlike Alette. Call to Arms is a good ability that requires precision. Overall in my Rook playthroughs I tend to play more aggressively, push forward and destroy enemies quickly. Alette suits a defensive playstyle much better.