Have an awesome trip! DisneySea is something special. The rides are great, but the park is first and foremost about the breathtaking way it transports you. Soak in the details. Some awesome advice in this thread by the way!
Tokyo Disneyland is no slacker either, but it's obviously not as unique. I'd say, since you're only going for a short time, you should probably prioritize Tokyo Disney Resort exclusives and exploration of DisneySea especially instead of attractions cloned in America.
A lot of the appeal of TDR is also the ridiculously good attention to detail and the Disney Cruise Line level service throughout the resort. The maintenance is flawless and the food game is very good at nearly all of the quick-service restaurants. The snack game is unreal.
Rides
Tokyo Disneyland Park
Since you won't have much time at Tokyo Disneyland, I would prioritize:
- Enchanted Tale of Beauty and The Beast (Disney Premier Access costs about $15 USD, allowing you entry to the FastPass line for a single ride, so honestly, given the crazy waits for B&TB, pull the plug on it for that ride)
- Pooh's Hunny Hunt (I haven't done B&TB but I love PHH. Do not miss it!)
- Monsters Inc. Hide and Go Seek (not elite, but unique!)
- Splash Mountain (simply the best version in the world, but is prone to huge wait times in the summer, that cool down in the evening)
- Pirates, Jungle Cruise, Small World, and Haunted Mansion all have reasonable waits, so they are probably what you're going to want to fill your day with in between these big rides.
Absolutely, under any circumstance, do not miss
Dreamlights, the park's night parade blows all the other ones ever made out of the water. Fireworks are skippable.
In terms of lands, I'd rank them in terms of beauty as (though, keep in mind this is very subjective)
- Beauty and the Beast
- Critter Country
- Adventureland (especially the market area)
- Westernland
- Tomorrowland
- Mickey's Toontown
- World Bazaar
- Fantasyland
Tokyo DisneySea
Do these two back-to-back in the morning. Be there at least 30 minutes before the park opens:
- Journey to The Center of Earth (its thematic design is something special even though it's a little short)
- Indiana Jones Adventure
Then, fill the day out with these shorter wait rides:
- Sinbad's Storybook Voyage (is generally a walk-on, but is widely regarded by theme park enthusiasts as world-class)
- 20,000 Leagues Under the Sea (it's not elite, but it is unique; waits are rarely top 45 minutes)
- Transit Steamer Line (the boat transportation around the park) and/or The Electric Railway
If you like, these are other exclusive rides, but I personally prefer both Toy Story Mania and Soarin' to them at TDS, but I would prioritize these two since they don't have stratospheric waits and the ride experience itself is unique to DisneySea:
- Tower of Terror (has a unique story/theme and the waits can get long though not crazy, although it is my least favorite on-ride version of the Tower of Terror, but I would do it over the next rides mentioned especially since it's exclusive)
- Finding Nemo: SeaRider (not elite, but unique. I don't really know how to describe this, it's like a completely underwater, tamer, Star Tours, and it makes for a wacky D-ticket)
I would re-ride Journey to the Center of the Earth or Sinbad before I'd ride TSM or Soarin'. Toy Story Mania! and especially Soarin' have the best queues of any of their respective versions, but I would definitely pass on them both since they frequently command 180+ waits which is absurd for any ride much less for two rides that aren't even headliners.
There's of course Big Band Beat, but like others have said, it's in a COVID B-mode. When it's operating normally, it's very well-done, and surprisingly, a lot of it is in English. To get on the bottom level, you have to enter a 'lottery' for it. The upper level has a queue.
I love the Venetian Gondolas (though the wait times can approach an hour), so you may want to skip it, but definitely walk around the Venice area. Aquatopia (a trackless, water, flat-ride) is also fun too, but I would definitely take the former over it.
In the big Titanic-like ship, there's a place called the Teddy Roosevelt Lounge, it's very cool, so take a look inside. Also, in the fort/castle in front of Mt. Prometheus (the volcano) Fortress Explorations is a delight, especially at night. Explore every inch of the park, everything is stunning, and even the Mermaid Lagoon indoor land is worth checking out (I'd skip every attraction inside, though).
In terms of lands I'd rank them in terms of beauty as (though, keep in mind this is very subjective, they all are incredible)
- American Waterfront
- Mysterious Island (the biggest wow-factor)
- Mediterranean Harbor (especially the Venice area)
- Arabian Coast (especially the market area)
- Port Discovery
- Lost River Delta
- Mermaid Lagoon
Your perception of the park would be different doing it in this exclusive sort of way than if you were doing it normally, obviously, but it likely makes the most sense if you don't plan on returning for a while, and if you frequent WDW/DL.
Things will also change real-world. If the Venetian Gondolas are under 30 minutes and you happen to be right there, it's definitely worth doing while if SeaRider is at 90 minutes it's definitely not, etc. So use all of the perspectives here as a starting point for your own adventure rather than a rigid set of rules.
One thing to note is that you can't hop in a queue in the minutes before park closing as the queues for the big rides will close over an hour before the parks officially do. The parks themselves usually stay open until around 10pm; this is due to most Cast Members needing to get home before Tokyo's rail system shuts down for the night, and is my
only gripe about the resort.
Restaurants
Food-wise, you are correct in saying you should skip table-service. If you were there for a long weekend I'd say most definitely, but not for a day and a half. Magellan's (table-service) at Tokyo DisneySea is arguably the best theme park restaurant in the world and is in the Fortress Explorations Fort, so you could take a quick look into it while passing by.
The quick-service restaurants are excellent. My personal favorite is
Vulcania next to 20,000 Leagues Under the Sea at Tokyo DisneySea and
Grandma Sara's Kitchen next to Splash Mountain or
Hungry Bear Restaurant in Westernland.
Be sure to check out the theming though at both parks' restaurants as the ones at DisneySea especially are SO well themed. From DisneySea's Casbah Food Court (in Arabian Coast) to Queen of Heart's Banquet Hall at Tokyo Disneyland's Fantasyland there's some legitimately stunning ones (Grandma Sara's and Vulcania are too).
The snack game is so good that it should at least replace one meal at each park (I would honestly grab some food after the park closes off-property to maximize your time at the parks, that's what I typically do). Speaking of after the park, definitely check out Hotel MiraCosta's lobby at Tokyo DisneySea. Now that is a treat!
Also, try to avoid eating during the lunch rush from 11am-2pm. A meal at 2:30pm with snacks holding you until around a 10:30 dinner outside the parks is the way to go. It will save you a good chunk of time.
Snacks
There are dozens of popcorn flavors spread across each park from strawberry to BBQ, and honey to chocolate, so make a point to try at least a couple! For non-popcorn snacks, the
Gyoza Sausage Bun next to 20,000 Leagues and the
Little Green Alien Mochi in Tomorrowland are both fire 
. There's far more than this, but the two websites linked below provide great guides into everything (including snacks) at TDR. I recommend checking them out!
Disney Tourist Blog &
TDR Explorer
Also, make it a point to download the Tokyo Disney App! You'll be able to of course check wait times but also buy Premier Access which you can only buy the day of.
One thing you'll also notice is that not only are the park tickets significantly cheaper than the other Disney parks, but the food is too!
Anyway, the resort is a real treat. They really are how all theme parks should be run, and DisneySea in particular is a global treasure. Hope you have a great time!
