There really aren't any Fallout 3 influences. Like, at all. The fact that they're calling them "perks" in Skyrim doesn't mean much, as they're much more akin to the skill trees you find in some action RPGs e.g. Diablo 2. The leveling system is still completely different, there is even more emphasis on action and combat, and there are no dialogue trees whatsoever.
There are many influences. Scaling system, stealth system,kids,perks(I know OB had them so this goes both ways),hand crafted world & unique towns(I know MW had these also, so its a bit of both), lack of dialog trees for less important npc's, likely use of skills during conversation(with out a speech mini game, I think it safe to assume they will use FO3 skill based dialog options to handle speechcraft). There is probably more, but you get the point. Todd even mentioned the influences.