I'm yet to see a 3D engine that didn't have clipping problems at all. Half-Life 2 has a very good attempt to it but it's not 100% working.
The Doom 3 technology has almost no clipping problems at all, but no engine can reach the 100% working border. But well, in RPGs this is one of the things i don't except. Story, non-linearity, character development are more important imho.
