Chelsea will have a much more difficult opponent due to the goal conceded in the 94th minute, they did rotate heavily for this game but still - conceding 3 goals against Zenit isn't something they should have allowed. They might regret it really soon.
Finishing second below Juventus is a blessing in disguse looking at possible fixtures at the knock out stage. They will most likely play one of these teams: Bayerm, Ajax, Real Madrid, or Lille. When they return to full strength, Chelsea will easily defeat the other teams. However, I'm concerned we'll have to face Bayern because we haven't had an easy knockout stage match since 2007.