Things that don't make sense (v2)

Just finished a trilogy run. I have many of these in mind, but I don't know how motivated I am to write them.

The importance of the Prothean Cipher is forgotten

It's pretty much ignored entirely in Mass Effect 2: there is the beacon message viewed during N7: Archeological Dig Site and the recovered sphere in Project Firewalker: Prothean Site, but if the cipher is meaningful in these two situations it happens within Shepard's mind and is not shown to the player.

In Mass Effect 3, the cipher comes into play in a significant sense twice: once, when trying to awaken Javik, and a second time when investigating the Temple of Athame on Thessia.

However, it is completely forgotten in other circumstances. Let's accept that what Shiala told Shepard on Feros is true: the cipher is the experience of being prothean. It allows one to understand the language, the culture, and the people. Shiala did say it would take time to fully understand it, of course, so some forgiveness may be given for the fact that Shepard had weeks between obtaining the cipher and the collector attack over Alchera. Shepard's mind would have had time to process the cipher after the Lazarus Project, however, but no progress on this front was ever made.

Here are some things to think about:

In Mass Effect 3, Liara is constantly complaining that she needs better prothean material to work with to help decipher the Crucible plans. Well, Shepard is the walking codex of prothean comprehension. The knowledge may not necessarily be accessible immediately, but it is there. There's no explanation at all as to why Liara doesn't gain the cipher herself by bonding with Shepard's mind. If Shiala can absorb it from the Thorian and share it with both Saren and Shepard, Liara should be able to do the same. Or if not Liara, another asari with Shiala's skill level. Liara, or whomever, could then share it with whomever was working on the Crucible project with the need of the knowledge. The majority of the prothean artifact collection assignments become instantly irrelevant. The Crucible is finished faster, or at least any phase that isn't dependent upon obtaining additional construction materials would be.

In Mass Effect 3, Shepard tells Javik that the prothean psychometric ability is puzzling. But that's just it. It shouldn't be. With the cipher, Shepard should either already understand it outright, or the first experience with it should have awakened the cipher memory so that it was then understood. The whole thing is a mess, likely because the writers needed to have someone be utterly ignorant of how it worked and that requires Shepard to ask questions, but Shepard is not the one who should be asking questions. Shepard should know.

Shepard's relationship with Javik should be much, much different than portrayed. Shepard would be the only person in the galaxy that would actually understand Javik, know why Javik's perspective is the way it is, comprehend the imperialist nature the protheans had. Even if Shepard disagreed with Javik, the cipher should have made Shepard someone Javik could at least feel more comfortable around.

In Mass Effect 3, Shepard shouldn't have to ask about the Echo Shard from the perspective of ignorance. Again, Shepard should know what the shards are, even if the specifics of the one Javik has are not known.

In Leviathan, while searching Bryson's lab, Shepard asks EDI if a particular artifact is prothean. Shepard should know this. If anything, EDI should be asking Shepard to confirm that it is prothean.

More example exist, scattered throughout the trilogy. These are the just the ones that immediately come to mind.