Not really, that was a tradeoff that needed to be made years ago, but not anymore. Modern rendering hardware can handle pretty much anything thrown at it, and it's all optimized to handle 3D meshes and textures and lighting and perspective. Isometric 3D1 is a big step backwards in rendering for no gain in performance. Isometric is ineffective for outdoor scenes and even large interiors, because even movable-camera isometric lacks any simulation of perspective. This makes it a suitable choice only for games where the view is tightly constrained, and undesirable for games where a high, wide, and handsome view of the landscape is considered desirable.
Fallout 3 is on a double-layer DVD, and it doesn't even fill two-thirds of it. There isn't a disk space issue. It's more a matter of having main and side stories that need a large, rich world to play out in, because no game developer who wants to make a profit will sacrifice development cost and time to market for a game that is bigger than it needs to be.
1True isometric projection (in which the Cartesian axes make 120-degree angles with each other) has never been practical for raster displays, because anything parallel to the XY plane axes suffers badly from aliasing. A pseudo-isometric projection in which the camera elevation is reduced to 30 degrees gives much better results. It is the latter which is commonly called "isometric", even though it is not.