Both have their pros and cons but i would go for a 3d solution as in my opinion it makes more sense for such a type of game. If you keep a certain viewing distance then you also don't need high res textures and so things still can look pretty detailed. If you have a fast terrain engine (something octree based for instance) this could be quite fast and for slower systems additional objects like trees could be rendered as billboards as well. Will be more work/slower depending on how you implement a path finding/walking system, do you make usage of the 3d terrain as well or keep a 2d collision map for this in memory and such things. It just gives you more freedom for both the look and the gameplay.
I don't think that a 2d system is slower out of the box as it depends on if the 2d is hardware accelerated and how you actually implement it, do you for instance just use blitzmax calls or do you put such calls together and make usage of internal openGL structures. Depending on what you do the trianglecount for the 3d version will propably be higher.
Anyway you have to keep in mind how you best generate the media. 3d will be a different way than 2d, so you should think about what fits best to you here too.
I don't think that a 2d system is slower out of the box as it depends on if the 2d is hardware accelerated and how you actually implement it, do you for instance just use blitzmax calls or do you put such calls together and make usage of internal openGL structures. Depending on what you do the trianglecount for the 3d version will propably be higher.
Anyway you have to keep in mind how you best generate the media. 3d will be a different way than 2d, so you should think about what fits best to you here too.