I don't think the preparation time is an issue. I rather think that playing in the second league works differently than playing in the first league even motivation wise. In the first league you could be competing for international competitions and have seriously motivating goals. In the second league it is all about do or die. If they don't advance to the first league right away, they are wasting the club's time in the second league for another year. Also, if you once played first league it's quite the change to now play against some of those unknown second league clubs. It won't be an easy season for Werder and Schalke.
Actually, it is at time like this that the professionalism of a player who has received a contract from a team will be tested. Team need to win and win so that the second tier competition is only the basis for a quick return to the main competition next season. But if the motivation of the players is lost and they are playing badly just because they can't stay in the main competition, then I think it's time for the coach to give young talents a chance to get more playing time. However, the two team were really bad last season and it's only natural that they should be in the second tier this season.
That might indeed be a good point. I think a young guy who is around 18 - 20 years old will definitely give his best as he has still goals and wants to present himself in the best shape possible in order to make it into the first league. I think it is much harder for someone who played first league for 6 or 7 years, then goes down into the second league and is now supposed to play his very best to return into the first league right away. Could definitely end in a motivational dilemma.