Well, just from the perspective of the narrative and the ending situation we have, the only way they can do any kind of sequel is to jump WAY far ahead in time (like whole new races) or give some kind of base ending import utility. Something very high level in which races lived and which ending you chose type of deal. Even then, it's hard to really have a threat unless you introduce some new threat from out of nowhere, and even then the scope of threat would be severely less. If they even tried, it would come across almost comical. So I'm betting prequel.
The reason to even write all this is to give you my side of your statement about choices. None of them work for me....for my Shepard and the choices I made. In fact, the two I lean more towards (although both still have issues) are the ones I would normally not choose or like the least. Again, perhaps this was in their plan but allow me to detail some of the conversation points.
Destroy: Does not work for a Paragon Shepard. I just brokered peace between Geth and Quarians, helped the Geth transcend into a race, and talked EDI through nuanced conversations about the nature of organic existence as she tries to make herself more "human". Turning around and choosing genocide for the Geth and killing a close friend in EDI to stop the Reapers? Well, it's a tough pill to swallow. The "derp derp" internet hordes who point that being the "true, good" ending seem to miss that point. Yes, it does allude to Shepard surviving, but the life of that one character doesn't equate to being the right choice. If you were a Renegade Shep, perfect. Heck, the default new Shep for ME2 or ME3 totally leans that way, making those kind of choices the default canon. It does accomplish Shepard's almost singular end-goal, but the variables have changed in the equation. If Shepard doesn't adjust to this new information, Shepard is no better than the Star Child. This connects heavily to the next ending....
Synthesis: Here is my problem with it.....I don't trust it. According to the Star Child, it's the final form of evolution. The starchild seems to believe it's the perfect form. It couldn't accomplish synthesis on it's own, so Shepard becomes the catalyst. OK, I see that. My argument is the source. The Leviathan DLC becomes key here, which again makes it upsetting that it was DLC and not deemed crucial to the story. Yes, you make the same choices in the end but the background of the Reapers (and heck even the "From Ashes" DLC with the Prothean story) become key story points which should guide your decision. Star Child is an Artifical Intelligence. Not a god, demi-god, whatever. It's a construct, a program given a problem to solve. And that makes it faulty.
Think on this, you write a program to solve the gun problem in America. You give it all the hard variables, all the facts. It decides that in order to solve the gun problem, it must destroy all humans. Does that solve the problem of gun violence? Yeah, because humanity is extinct. But is that the
right answer? An AI just understands solving a problem, not any ethical repercussions of its choice. And the Reaper Star Child AI is just that. Creating a solution, no matter how much worse it is than the problem. And in the extended cut, Star Child refers to Synthesis as the ultimate solution. The inevitable and perfect choice.
Further to this point, the AI has been proven wrong in this cycle. Synthetics (the Geth) didn't rise up and rebel against their creators. That was the point of that whole Geth-Quarian mission in ME3. You learn they were defending themselves from the Quarians. And when they drove them off, they didn't seek out further violence. They hid themselves away, and they even showed the first signs of independent thinking when some of them sided with Saren and Sovereign. It was a split among the Geth, when they should all be of one mind. But they came up with two solutions and caused a rift.
Connect this to Javik. In his time, the Protheans were a master race, much like the Leviathans who created the Reaper AI. Machines were not to be trusted and rose up against organics. But that cycle has been broken now. My Shepard brokered peace, the Geth are advancing on their own and now peaceful with their creators. The problem the AI was created to fix does not even exist. EDI was the AI from Mars that struck out against humans, that's because of how Cerberus was affecting it and making it self-aware. But she has transcended that existence with Shepard's guidance and her connection to Joker.
That is a long way to say that if this is the preferred choice of the Reaper AI, I don't trust it. Shepard is making a massive decision for all life in galaxy, changing their entire DNA without their consent or input. Evolution doesn't consent either, but it happens naturally and over time. This feels wrong, like a promise of Utopia. All races suddenly become infused with Synthetic connections, and transcend to this perfect state along with the restoration of all the previous races consciousness in Reaper form? It's the end of evolution, no more struggle, no more perseverance, no more hope, no more art. Everything stagnates, and thus ends. Shepard asks why it wasn't done before, Star Child vaguely says they tried and failed. It cannot be forced, organics were not ready. Well....just because Shepard is doesn't mean all organics are ready, that is forcing it upon them.
The Rejection ending: Shepard chooses to not force one of these endings upon the galaxy, which honestly kinda works for my Shepard. It's rejecting that this is the only possible end (i.e. some other solution could present itself, this is all indoctrination theory, etc). Too bad Bioware made this the
you ending. You don't like our endings, fine. Everyone dies. You happy now? Real mature Bioware. Assholes.
Control: The Shepard becomes Super Jesus ending. Why it doesn't work: Because it's too big. We're not meant to control it. That is what Shepard says to the main sub-enemy of Mass Effect 3 in the Illusive Man. And it shows that I.M. is under Reaper control, indoctrinated. We can't seize control of them, we can't try to wield their power and own them. It's in the face of everything Shepard has said to indoctrinated foes from the beginning. So yeah, it's OK now. Shepard is here, so that must be kosher. WTF. Shepard dies, but his/her memories and focus basically rewrite the AI. Shepard becomes the Catalyst. No longer human, but his/her motivations as one now provide the Reapers directive of preserving all life, synthetic and organic. In that way, it's the ending that works most for me. Even though it's the one that not more than 10 minutes prior to choosing that SHEPARD HIM/HERSELF says is impossible. The best I can say is that Shepard getting there, free of indoctrination and imposed will proves to the AI that the solution no longer works and a new one must be chosen (as said by Star Child). And at this point, the AI is willing to accept a new directive. It has no self-preservation interest, it has no evolution of perception of itself or life unlike the other synthetic races in the game. It saw Shepard as a threat since if it beat the Reapers than the cycle would only continue unchecked. With control, it's technically still working to solve the problem....just allowing Shepard to be the controlling influence on how. The problem there becomes if this new focus becomes too singular and causes a similar situation where it corrects a problem in a horrible way.
So you see....in the end I was one of the "raving uneducated masses" that hated the endings initially. You know, because I thought about it. The indoctrination theory was a huge hope for me. So in the end.....le sigh.