When doing interplanetary missions or any missions around planets with atmospheres, can we specify the final Apoapsis that we want around the planet and then MechJeb calculates how close it need to pass by the planet (Enough to enter the atmosphere to slow down enough for the apoapsis of the specified amount, but not enough to de-orbit the craft) And then it will then circularize when it the gets to the apoapsis.

Is this possible or am I just dreaming.

With the current drag module, probably considering it's just chaining in the atmospheric predictions. The fact that the aerodynamics model is so simple is what lets them give us those predictions. Once they improve it, we'll have to take into account orientation and what not for the same reason that right now fairings don't reduce drag in assent. Maybe they'll be able to include an aerobrake/capture autopilot, though I assume things will get much more hands-on when squad improves the aerodynamics model.

It would be nice if MJ knew about aerobraking. Trajectories mod could be used for predictions.

It is particularly fussy to do the dance of aerobraking at periapsis slightly, then coasting to apoapsis, then adjusting periapsis, then aerobraking, wash/rinse/repeat. I would like a button to just do that for me.