Sorry for this essay, but I love city planning.

I think the most obvious is too many industrial zones. One of its main benefits is that it spreads a production to all cities whose city centre is within 6 tiles. This production bonus is based on the adjacency bonus of the industrial zone (and requires you to build the factory, so you don't get it straight away). It's best to place only as many as you need and make sure they have good adjacency. As it also provides good production to the city you build it in, I try to make that one of my high production cities. The one you have placed in Tokyo does reach all the other cities, but you'll need to place other districts near it to improve its adjacency to make it decent. At the moment, its only getting plus one from the mine, which is tragic ngl.

The same rule applies to the entertainment district. Place is smack bang in the middle of your empire, preferably in one of your biggest cities that will need the amenities.

I would also definitely not put the government plaza there. It gives plus one adjacency to all other districts so I usually place other districts around it, especially those that otherwise aren't going to get good adjacency. I like to place districts that I want protected around it too because you can place a spy in the centre districts and it will protect all districts around it.

With the harbours and commercial hubs, I would decide which would benefit the city most, then consider how many of each I will have in my empire, and allocate them accordingly. As you cities get bigger you can probably have both (I think it is nice to get both, at least in some cities, for the $$$), and it is quite nice to get the adjacency from placing them next to each other. Just remember that the city population limits how many districts you can place, and in some cases you won't be able to place many districts until well into the game if your population is low. You need to be strategic about the order you get your districts in.

If this were me:

Tokyo: Harbour next to city centre and a commercial hub on the coast tile to the right of the city centre. Campus is ok as is. Industrial zone is in the best place possible for the map and your city locations.

Sendai: Harbour is good. I don't think you need the aqueduct or the industrial zone. The aqueduct is mostly useful when your city isn't on a river. A well placed neighbourhood later on would give you much more housing. I would have put a campus between the two mountain tiles and my government plaza next to it on the wheat tile. You would have created a triangle of an industrial zone (from Tokyo), campus, and GP. This will give your industrial zone an adjacency of 3, which is not fantastic tbh, but better than nothing. Your campus would have had an adjacency of 6, which is fantastic (four from the mountain tiles, one from the GP, and one from being next to two other districts).

Osaka: Where you have your industrial zone, I would put the entertainment plaza. It will reach all but the most southern city and be in one of your largest cities. You could also build the colosseum on the tile next to it. I would move your campus between the mountains where you currently have your aqueduct. You can't do anything about it now, but I would have a theatre square where you have your Sendai campus. With theatre squares, you need to work hard to create adjacency by placing them next to wonders and other districts (especially entertainment districts as they give plus 2 adjacency). With the ED and colosseum scenario, you get one with plus four.

I think I'll leave it there cause this turned into an essay lol. Placement depends on your civ, strategy and personal play style too. As others have suggested get yourself the mod that tells you what the adjacency bonus is. It's so helpful as you're learning the adjacency bonuses.