Fears for ME5. Obviously there may be spoilers!

Oh, I'm sure they'll find a way to keep it, if for no other reason than a ham-fisted way to lecture the audience on how much BETTER things are now.

Hell, the Ryder-SAM thing always struck me as a not so subtle jab at how Synthesis is AWESOME!

Right, they kept EDI shackled, and Miranda was seriously p*ssed when Joker released her.

I don't know about that.... After all they were founded by a guy who is a meat puppet of the robo squids and do experiments on humans (on the orders of said meat puppet) when they could use the council races for those experiments instead...

We learn it when talking to Gianna in ME1. You have to ask her about the corporations on Noveria. Shepard then mentions hearing about Synthetic Insights in the news and Gianna says they are one of four groups the Council allows to work on AI.

Right, you need specials permission from the Citadel Council to research AIs. Thus far, only four groups have that permission (and they take extreme precautions to make sure they can't escape)

Researching AI is heavily restricted, and requires special permission form the Citadel Council. At the time of ME1, there were four organizations that had such permission. We don't know what the other three are ( I believe) but one of them was the company Synthetic Insights., which is mentioned in ME1 and ME2

It's also mentioned in a conversation with Gianna Parasini in ME1 (since Synthetic insights had an office on Noveria)

Was SAM supposed to be a true AI, or was that something Alec worked on on the side?

When Alec was working with SAM under the Alliance it was illegal. That’s what got him dishonorably discharged and Scott and Sara blacklisted. After that he continued his research, reaching out to people like the ones we see, and eventually the Mysterious Benefactor approached Alec with the offer to join the Andromeda Initiative and continue his research.
The true potential of this particular SAM was kept under wraps, but the others were allowed since they were extremely shackled.

I think it can be two main differences:
1. Security. Groups like Synthetic Insights or the Andromeda Initiative develop their AIs in very controlled environments where they can’t pose a threat. Meanwhile Alec was creating SAM with seemingly none of those security measures.
2. Reason: Synthetic Insights works with AIs to develop VI systems for mechs or things like the greybox which had the goal of being a way to defeat diseases like Alzheimer’s. The Andromeda Initiative works with AIs to serve as a tool to react to any situation, from almost instantaneously understanding new species to problems or situations that need to be addressed immediately when colonizing. Both proved that they needed AIs in order to do these things. Meanwhile Alec was talking about merging AIs into people which could be seen as a way to make an army of super soldiers, unleash AI into the galaxy, etc. Hence why he keeps his work on our SAM secret even from pretty much everyone in the Initiative.

Which is weird because synthesis is directly at odds with what Javik told them about a race in his own time. The AI/organic meld ended with the organics dead. But them I'm a proponent that Reapers can't be trusted to exist and I think they had a hand in the zha/zha'til mess.