Here's a prediction: After defeating the Reaper threat, Shepard and the Alliance go all out and kill the Illusive Man.
Mark my words.
The Reapers will the the Main Threat & defeating them(if you get the good outcome) will be the last thing you do.
Cerberus Plot might be ending around 65% to 75% point of the game. 45% to 55% point of the game will most likely be Shepard going head to Head with Kai Leng.
It seems the Alliance will be giving you Intel that will help you track down the illusive man. It would than be Shepard, Miranda & Jacob Hunting down The illusive Man & Destroying Cerberus(or atlease the Lazarus Cell).
I just hope the deal with Love Interests properly. Not just put it on the backburner.
Liara & Shepard fulling what they said at the End of Lair of the Shadow Broker.
Miranda would be Finding a Cure or a Fix for Miranda so she can have Children(since she wants to have Children).
Thane would be finding a Cure for his illness so he can live( if he is still alive). I know the Actor who voiced him said EA & BioWare has yet to contact him about doing voice work(yet?).
Tali would be trying to find a Home World for her People. Since Cross Race breeding is not possible with Humans & Quarians.
Samara(Semi-Romance) my best guess is trying to convince her to quit the justicar Order & to be With Shepard.
Ashley, Jacob, Kelly(She is considered a Semi-Romance), Garrus, Kaiden really don't have Major issues with them.
Wonder who the new Love Interests will be? Most likely it be James Sanders & a unannounced Female(maybe Kahlee Sanders or Gillian Grayson).