Many people use Toyota, more than other brands in Nigeria, same people abuse their vehicles heavily. Part sellers will stock parts that in high demand, which happen to be Toyotas.
Most used engines in Ladipo are rebuilt, not just Toyota engines, don't take my word for it, just walk around the market. Except you are buying directly from the container, and you have to know what you are doing to be able to. And yes, more Toyota engines are rebuilt, because there is a higher demand for it.
As a first time car user. You are safe with known brands if you will be travelling a lot within the country. Getting a Toyota, Honda, mechanic won't be hard.
If you want to use the vehicle for transport. Check the route you will be using, what vehicles are common. Even within a state, there are particular brands used there. For example in Lagos. Epe, Ajah, ibeju axis: Opel Zafira, Korope : Itoikin Ikorodu axis: Mazda mpv, Ikorodu to Oshodi axis: Volkswagen bus, mazda bus, etc. If your vehicle breaks down along that route, you are sure of getting a mechanic to fix the problem.
Generally, it is car users that are brand loyalist. The manufacturer across board buy parts from largely the same manufacturer and assemble. That is why the base price for new vehicles in the same category are just slightly different. They adopt and improve on the same technology.
But whatever you like.