I don't think you can compare Kojima to Ken. I think you can compare Kojima to Todd. Anyway, until reading some post I really had no idea that Ken was not all that involved in Oblivion. With that being said I don't think it will make any real difference on the game.
Personally, I think the only thing the game can do it get better. I am sure they have learned from some of the mistakes in Oblivion and are stiving to make another game that blows everyone away. I would like to say Oblivion was better than Fallout 3 but that is like comparing apples and oranges. They are both great games and I am sure Skyrim will go above and beyond all expectations.
To some older fans its not even Todd, see below for the The Lefay Factor. For me its Ted who basically created the system still in use today
Ken did a lot of not so good things with his silly rules.
A paranoia dev saying no betrayal? How many quest options does that cut out?
But wait it gets worse no lying to the character if the NPC had been honest before - wait what
Everything having to have a real world counterpart - not that bad per say French Britons - Roman imperials - but it needs to be a constant in other games and in some respects it ignored canon
which brings us to --- Ignored lore and canon and directly contradicted even himself
Gutting the character system
Replacing a perfectly good combat system with a shockingly bad one
there are others but to me theres where the man offenders in Morrowind
Pushing level scaling -----lets not go there, they could have just made sure there was playtested content for high levels with the best gear or how about challenges that are not about combat stats and gear
Ken has done some good stuff in his time, interestingly his part of the enemy Within is considered the worst part (it is hampered by following Power behind the throne - which is the best RPG adventure module ever) because it was a paranoia hose job for Warhammer - looks like he took it too far by removing it all not understanding that its not a hose job or betrayal that is bad but an over the top paranoia style really only works in Paranoia and we see this trait again in Oblivion not taking the middle ground but taking some criticism and using a sledge hammer OTT solution because the criticism is not always fully understood
Edit: Oranges and apples are both fruit, an orange's color is really a one dimensional thing hence its name where as an apple can come in many shades of red, green or yellow. Both are covered in skin, in an orange this is referred to as a peel and is too bitter for most peoples tastes, the apple skin is much less bitter. both are seed containers in their natural function, the cases in both are edible, the flesh of both is quite sweet although in the case of apples the sweetness can vary. The point- you can validly compare anything to anything especially two games made by the same company and designed with the same philosophy "comparing apples to oranges" is a faulty premise to brush off unfavorable comparisons especially when said comparisons are valid (as a side note the phrase is "chalk and cheese" and while that makes more scene they can still be compared). Without comparison between games cross genre even games will not improve