So as we all probably now know in ME3 Shepard will find a living Prothean that survived the Reapers last cycle. Now in my opinion this presents some problems that I worry Bioware might overlook (you can list your worries as well).

  1. First is the obvious one regarding their appearence. We now know they look like Collectors, but the statues on Ilos suggest otherwhy's, this is somthin bioware will have to explain in game and I think it would be wise of them for Shepard and Liara to make that observation.
  2. is that because of their appearence (well his) it would be silly for Shepard, Tali, Garrus and mabye even Liara and the Virmier survivor not to think he is a Collector that somhow survived their attack on the base.
  3. With Liara on you sqaud it would be realy stupid for there not to be any interaction between her and the Prothean (She is the expert).
  4. At the Ilos facilaty a warning is played (in the Prothean language) that only Shepard understands because you got the cipher which inabled him to understand Prothean. In Mass Effect all races have translaters that allows them to speak their language and a member of an other race to hear it in theirs. Since the Prothean is just awakened from status, he will not have a translator so it will be stupid for him to understand Shepards squad(unless of course he is out of status when Shepard meets him and he has been able to get a translator) and Shepards squad to understand him, however with Shepard having the cipher he will understand what the Prothean has said and mabye the Prothean will understand him because of it.

I will add more if I can think of any.

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