I suppose the show hasn't really paid attention to the fans and is still featuring a lot of Lincoln. :(
The episode description for episode 4.09 "Enemy of my Enemy":
FRINGE DIVISION FACES NEW CHALLENGES ON AN ALL-NEW "FRINGE" FRIDAY, JANUARY 20, ON FOX
Peter's visit to the other side intensifies as the alternate FRINGE division faces off against a formidable new foe in a harrowing race against time in the all-new "Enemy of My Enemy" episode of FRINGE airing Friday, Jan. 20 (9:00-10:00 PM ET/PT) on FOX. (FR-409) (TV-14 L, V)
So, it seems that Peter is still in the Alternative Universe during the course of both episodes. Episode 4.08 and 4.09 will probably be a lot like Over There I and II. I just hope that they both feature Peter more!