That's my point - wanting what he can't have again. As for your season description, here's mine:
S1: JD has a crush on Elliot but realises in the third episode that choosing friendship over sex in this case makes sense. When they do hook up after Elliot realises she's jealous, JD realises he can't make the same jokes he used to when they were friends and Elliot couldn't let the little things go. They fought constantly and mutually realised it wasn't working and after some time became friends again. However Elliot still has lingering feelings since they didn't have enough space after the breakup.
S2: Elliot gets over JD but when JD realises that he's sexually attracted to Elliot again, since his peep started working again, they both had a Christmas present of sex, involving biting ass. When they remember how terrible a couple they were, they decide to remain friends who hook up to relieve stress. However, this distracts Elliot from her work so they break it off, just after JD realises he still loves her. Both move on and have relationships, J.D. with Jamie, and Elliot with Paul, and both are fine and over it.
S3: JD sees a change in Elliot that sparks his interests again, soon before seeing her with Sean, which made him over jealous so he starts dating Danni but is not fully into the relationship. So he then hooks up with Elliot while Sean is in NZ, but Elliot is only doing this because she's confused about the long distance relationship (which I hope is not repeated in this season - Elliot's confusion of a relationship causing her to hook up with JD). When Sean comes back, she chooses him and JD is crushed but still has feelings so convinces her to break up with him but realising that he was jealous because he missed their relationship, not because he still loved her so when he hears Turk's definition of love he breaks it off, causing a vicious move by Elliot and for her to basically loathe him until over time she forgave him and thay became close friends again after realising neither have romantic feelings for each other.
(Part of that was season 4)
S6: Now that Elliot's in a serious relationship, J.D. is jealous, both because he missed out on a serious relationship with Kim after her "miscarriage" and because it could have been him Elliot was marrying if she still loved him. When Kim confronts him at the hospital on why he ran from responsibility and Elliot asked him what he thought of the wedding... (to be continued)