SPOILERZ!

Mordin though, read that he will die regardless whether u choose paragon or renegade option.

Phew... Luckily I am playing a renegade and like Grunty more than the bug

You can save both and make them war assets?

is good at repairing thing..in other owrd, when it come to engineering, rachni is brilliant. you'll see they only help the enginering on the Crucible..i was expecting they are on the front line given Rachni is damn ferocious as a frontliner

The protheans forced other races  to submit to them or be destroyed.  This is the reason why the protheans remain the only space-faring race in the last cycle - by force.  If the reapers didn't destroy the protheans then, humans will be slaves to the protheans in the current cycle.
However, this is admitted by Jarek to be Protheans' weakness because there was no diversity in their cycle. Once the Reapers attacked them, they don't have any new ideas to counter them.

The current cycle in Mass Effect is very diverse, with AIs like Geth and a democratic system spearheaded by the Asari Empire. It created lots of war between them, but they have diversity in opinions and technique. This is the strength that Protheans lack.
I think the Catalyst perceived humans as the first being who proved them wrong, that their solution to the violent synthetic-biotic does not work anymore.  It's due to synthetic-biotics cooperation that Shepard (shepard was also a synthetic-biotic cybernatics) was able to get into the Crucible to talk to the Catalyst, something unimaginable for the Creators of Reapers (who might be so ravaged by AI destroying bio organism). The Catalyst see that AI and Biotic organism can actually co-exist and defeat the Reapers. So the Catalyst was 'wrong' and realized it. Therefore, it gives a choice to Shepard to destroy the Reapers for good, along with their technology.

In some ways, the galaxy now will chart their own ways independent of Reapers' influence. With that, the technology the reapers give them will also have to come to an end.

It's really a very epic ending if you think about it.

I think it's unlikely the writers would introduce conspiracy theories or indoctrination. I mean, if Shepard was indoctrinated - the story is not finished. It would make a joke out of Mass Effect trilogy series. The producers were very clear to say that Mass Effect 3 will wrap up Shepard's story.  I think they DID wrap up the story , not to everyone's liking.
The indoctrination theory is just a coping mechanism by some fans which refuse to accept the devastating ending...  Let's say that Bioware is really suggesting indoctrination of shepard, they must have thought about a DLC. But if they do that, it will make other fans angry again because Bioware would be seen to deliberately leaving out the ending of the Mass Effect 3 for a future DLC.

There was a already a big fuss about Bioware craving out the Prothean story as a DLC. It won't make Bioware look good to do another DLC for Mass Effect 3 ending proper.

But as gaming industry is very much driven by money and commercial demand, Bioware "may" just concede with fans request for a 'happy ending'.  Honestly, I am a sucker for good endings, and yes I would purchase the DLC for a happy ending....

Yea, the part about Shepard found below the rubbles didn't really make sense too. The citadel was destroyed and there was no way shepard can survive re-entry into the atmosphere without being pulverised.

Maybe Bioware is just testing the water whether there will be commercial demand for a DLC, another way to milk more money from fans...