I definitely agree with a lot of what everyone above as stated. For me specifically I'd like:
1. Cure Cosima. Cosima cannot die! I'd love to see Cosima use Ethan's notes and Helena's babies to find a cure.
2. more of the clones interacting with each other and not only with Sarah. Would really love to get Cosima/Alison/Helena/Rachel (if she survivied) combinations (not all together but in some shape or form, like Alison/Cosima, Alison/Helena, Cosima/Rachel, etc.), even if only via skype and phone calls.
3. Bring Delphine back- and make her mor integral with characters other than Cosima.
4. More Alison/Felix
5. Male clones dont overshadow Clone Club. We already have Sarah, Alison, Cosima, Helena, and Felix. Then there's Rachel (maybe?), Charlotte and the others who are interesting (Mrs. S, Kira, Delphine, Marion). I love the idea of male clones, but i dont want them stealing screen time from the characters we already sortof know.
6. Real answers about DYAD, Topside, and Project Castor. In fact real answers in general. I want to know about Siobhan, Marion, who the original is for Project Leda and Project Castor. Why the original(s) were important enough to be used in cloning. Does the sickness stem from the original, the process of cloning, or the synthetic genome in their DNA? Were the original(s) sick? Are clone club and the male clones related or just similar in nature (the fact that their clones)
7. Baby clone (Charlotte) meeting her big sisters (not just Sarah); Charlotte meeting Kira
8. Kira meeting Allison's kids; Allison's kids meeting their "aunties"
9. No more kidnapping Kira or Helena, it's starting to get old
10. Either give Cal an actual personality/storyline or cut his screen time, same with Paul
11. Donnie becoming important now that he's in the loop.
12. We know Cosima has an ID code (324B21), and we're assuming all of them do (its how they keep track of each clone and differentiate), but since Sarah and Helena are accidents (identical twins), do they share the same ID number?
Obviously, I won't get it all, however, I hope at least some of these will be featured in season 3, especially Cosima's cure, Clone Club interactions, question answer, baby clone, and Delphine.