By gameplay mechanics, do you mean because FO3 was 3D while the previous games were 2D? Not that I really see a TES clone as a bad thing, since TES/F3-style gameplay appeals to me as a gamer.
EDIT: I suppose this is getting off-topic. There are other threads for that issue, so I won't go on F3 gameplay.
3D an 2D are not factors in this. The original Fallout 3 was going to be 3D and would've still maintained the aspects in the core of the series gameplay (RPG mechanics, map-node system, higher focus on writing and storytelling, TB combat - also including realtime combat).
I don't think Interplay can, in its current state and management, do any better than Beth with Fallout 3... although, I do have a neutral stance since Interplays game would like be different from what Beth does (aka, not a TES clone - as Fallout is, afterall, Fallout and not TES).
Anyway, as the lawsuit is ongoing, and threads discussing it have all been locked so far (not sure if policies have changed since the last thread).