The Madrid Card is time-limited. Having struggled last year to cram card-related sights into the validity-period of the Berlin tourist card I had purchased, I am now biased against cards with limited validity periods unless the period coincides with the traveler's stay in the city. I like some flexibility in my schedule. If it's a beautiful day, why would I want to go to 2 or 3 museums? And if I'm loving a particular sight, I don't want to rush out in order to make use of the card at another sight.
As an alternative to the Madrid Card, there's the Paseo del Arte pass, which covers the Big 3 museums (Prado, Thyssen and Reina Sofia), though not special exhibitions at the Thyssen (not sure about the other two). It costs about 29 euros and is valid for one visit to each museum over the course of one year.
However, you need to consider not only the costs of the pass and the (alternative) individual tickets, but also whether the ability to skip ticket-purchasing lines would be helpful (perhaps at the Prado, but not sure about October/November) and whether you might be able to take advantage of a free-entry period at one or more of the museums.
The Prado is free from 6 PM to 8 PM every day. It's a very large museum; it certainly cannot even be skimmed in 2 hours. But you could choose some individual sections and see them in that time, or you could make more than one free visit. I hit two free days in mid-May and found that, though the museum was busy, the only two paintings with large clots of people in front of them were Velazquez's "Las Meninas" and Bosch's "The Garden of Earthly Delights".
The Reina Sofia is free Monday and Wednesday-Saturday from 7 to 9 PM (closed Tuesday) and on Sunday from 1:30 to 7 PM (though some collections are closed then).
The Thyssen's permanent collection is free on Mondays from noon to 4 PM.
This web site purports to list the free-entry options for many Madrid museums. To be safe, you should verify this information on the museums' official web sites.
There's a similar situation in Barcelona, with a number of sights offering free-entry options. The usual recommendation is to use such times at relatively low-traffic sites. Barcelona has more sights that are subject to long ticket lines (La Sagrada Familia, Parc Guell, Picasso Museum and La Pedrera; perhaps also the Museu Nacional d'Art de Catalunya, Casa Batllo and Palau Guell), but unfortunately most of those are not fully covered by the Barcelona Card, so the line-skipping possibilities are limited. I think the purchase decision is basically an economic one.
The Barcelona Card provides discounts at a number of the modernista sights, but I think you have to buy your tickets at the sites in order to claim the discount. That means standing in line rather than buying an online ticket or picking one up at the tourist office ahead of time. So the card may not provide much value there.
The card's 50% discount on the tourist office's walking tours could be worthwhile. I took and enjoyed the Picasso, Barri Gotic and Modernisme tours. The Picasso tour includes entry to the museum (no worry about the line) and you are free to remain there after the tour ends. The tour doesn't help with the crowding, though.
If you don't care about early Picasso, I'd skip the crowded Picasso Museum. The Miro Museum (free with the card) is modern and uncrowded, but it is also basically a one-artist museum. Don't care much for Miro? Go elsewhere. I found the Museu Nacional d'Art de Catalunya not overly crowded even during free periods in August.
Don't over-value the local-transportation part of the Barcelona Card. You can buy a T-10 ticket (10 rides, or 5 rides of 2 people) for about 10 euros.
Multiple posters here have been happy with their pre-booked early-AM entries to La Sagrada Familia. I can't comment on the towers.
