You look at the popularity of the ride (measured by utilization) against it's "cost per guest carried", or the average of the staff and upkeep against the actual ridership.
I kinda feel that this sort of thinking makes sense for large factories where they are making widgets, but Disneyland thrives because it has a plethora of rides which are both high quality and very varied in terms of guest experience. With such a layout, it is inevitable that some attractions will cost more to build, or maintain than others, perhaps by multiples. We know what cheap amusement parks look like, they buy roller coasters and cheap thrill rides and lightly theme them.
The Subs were a VERY high operation cost combined with a low capacity, making the cost per guest carried very high. When a major rehab comes along, like "reinforce the entire lagoon", then it does not make sense to keep the ride and they do something else or nothing. In WDW it was nothing, in DL it was Nemo.
There are stories that WDW maintenance/management got ride operators to make it look like the subs were falling apart when the brass toured them due to internal complaints with maintenance. They put water in one sub and pretended the thing was falling apart! So, I think there is a difference between high maintenance costs and rides that maintenance would rather not having to maintain. Supposedly, the high cost of the subs is the projector bulbs, $10,000 per month. Well, now in the 21st Century they have projectors with long lived LED light sources. So, eventually when they do a refurb the Subs will cost less to operate. The electric motors are certainly costing much less to keep going versus the old diesel engines.
They believed Nemo would bring more guests to the park which justifies the spend (In Nemo's case, the huge spend was actually dis proportunate to the small capacity by a large margin, but that was John Lassiter chiming in).
It is just like with Tony Baxter/Treehouse/Tarzan only . . . Nemo made the company billions when you consider merchandizing, and Nemo 2 will make billions when you consider merchandizing. I'm sure Nemo 2 will get a $200 million dollar marketing budget, at least . . . I think having a Nemo ride in Disneyland is synergy with the films, and they will push a lot of Nemo merch and stuff in the park.
If they cut Nemo, then logically they could cut the train around the park, a high maintenance ride, but perhaps not with the ridership guests want? Of course, a lot of folks would hate this, as the train is such an integral part of the park. Even if you miss the train on a visit, to just see the train pass through the station as you enter Disneyland . . . it's starting a movie with an awesome action sequence, like in the first Indiana Jones.
BVS is a carefully measured half-a-teaspoon of magic, you've got the Red Car Trolley (perhaps even lower ridership than the subs), and shopping and a recreation of a building that was torn down decades ago. Not saying that the Carthay doesn't have a little charm, but there is a reason it got junked and why medieval castles are still standing and are heavily visited in Europe.
Everything in BVS and the non-Carsland DCA looks like the history of budget cuts writ large. You've got Mermaid with a couple upgraded animatronics . . . inside of a warehouse with cheap plastic fish, almost saying, "We'll let you look at two Ariels, one Ursula, and be happy about that and overlook everything else.
In the same vein, I think most guests enjoy walking by the sub lagoon, even if they aren't able to get on the ride during their visit. It sends a message that management is keeping things running. When Nemo 2 comes out, I'm sure everybody and their cousin will want to ride Nemo after/before seeing the film. They could even add some new surprises.