1.  The reason for the catalyst is because apparently conflict between synthetic and organic life is inevitable.  However, in the game you only see evidence to the contrary.  If you play your cards right, you are able to broker peace between the Geth and the Quarians.  EDI, an unshackled AI, is a valuable ally to her human crew.  The conflict between the Geth and the Geth heretics show that even with a purely synthetic world, peace is not a given.  Conflict can exist even within a hive mind.

The starchild says that the conflict is inevitable, and you just have to go with it.  In the DLC ending, you can challenge him on it, but he shuts you down.  This is odd considering you'd been able to change the mind of every major villain (Serin (sp) in ME1, the Elusive man right before) in the game to that point.

2.  The DLC ending isn't a new ending per se.  It's basically a fleshed out version of the original.  There is more conversation with the starkid, and an epilogue at the end.  There is also a scene showing your crewmates getting saved by the normandy when they rush the citadel.  It was offered as DLC originally.  I think it was built into future versions of the game.  

You can also completely reject the starchild or shoot him, but that basically leads to the developers saying "go fuck yourself".

The ending didn't go into anywhere near enough detail before the patch. The starchild just gave you three options with little real explanation (it was just about enough to understand the basics for the ending to work) and you picked one of the three. You then saw what happened to Shephard, the Reapers, the Mass Relays, and a vague end to the Normandy and crew. 

It didn't show the effect of any of your other decisions throughout the course of the trilogy so smaller decisions and even major ones just got sidelined leaving you with numerous questions as to what happened with x, y and z. In the patched ending they at least addressed that and showed the effects of even relatively minor decisions and gave more detailed stories for the more important characters. It improved things a lot, but it was still a little too simplistic for many. 

Personally I don't have the hatred many have for the ending. I enjoyed it for what it was and understood the point the developers tried to make in that some things are inevitable (in that Shephard always dies no matter what). 

That said, it was a bit too simple considering the complexity of the trilogy, but I'm not sure what else they could have done that would have made for a more satisfying ending. 

They've been doing this for countless years. Do I really believe this would be the one life cycle to get it right? The point is even though you negotiated peace it would fall apart. Just like in the real world. We've had peace with nations then we go to war with them. Also you see plenty of conflict between organically and synthetic. You basically made up the "only see evidence to the contrary ". You see evidence of both but in the end then it said it always leads to synthetics ruling.

*Spoilers*

Was the point the developers trying to make that some things are inevitable?  Again, we only have evidence to the contrary.  In ME1 it seems pretty inevitable that the citadel will fall, but you overcome impossible odds.  In Mass Effect 2, you go on what is constantly called a suicide mission, but you are able to make it out with all crew members alive, if you make the right choices.  You're able to end the genophage, end the seemingly endless battle between Geth and Quarian, overcome the reaper's mind control in several cases, etc etc.

So, Shepard routinely does the impossible.  The whole series is about ending a cycle that has been going on forever.  If the point was that certain things are inevitable, that would be a strange and sudden shift.  And of course, in one ending it seems that Shepard lives, so that throws another wrench in it.

As for what they could have done, the indoctrination theory, whether it was ever intended or not, would have been pretty satisfying as an ending.  Either that, or they could have just kept it simple, and had the united force of the galaxy defeat evil.  They would have had to change some things along the way, but it would have worked.  Wouldn't have been the most creative thing, but sometimes it's fine just to blow up the death star and have the good guys go home happy.

I'm not talking about the real world.  I'm talking about the game. *spoilers*

First off, the game makes a point of countlessly emphasizing that this cycle is vastly different at least than the protean cycle.  It is emphasized throughout the series that humans in general are and Shephard in particular is special. The very fact that your cycle is able to construct the catalyst is proof that your cycle is unique.

The star child says it always leads to synthetics ruling, but we have no reason to trust him.  When you confront him, he tells you that literally minutes before he was trying to deceive the illusive man into acting according to his will.  So we know he's willing to lie to humans.  He's allied with the reapers, and if you shoot him he'll speak to you in a reaper voice.  There are a lot of characters who lie.  

But, even if the star child is absolutely convinced of this, that doesn't make it true.  Maybe he's seen it happen time and time again, but we haven't.  The game can't constantly show me that conflict is not inevitable, then have a deus ex machina at the end tell me it is.  I mean, they can do that, but it's shitty writing.  

I didn't make up the "only see evidence to the contrary".  I made the claim, and backed it up with several examples.  If you can present a counterpoint from the game, then go for it.

That's only if you play your cards right though, and then that's only via Shephards (your) influence. Without the player influence then synthetic life and organic life were in a constant war with each other. For instance, EDI was originally a rogue AI that could have slaughtered hundreds without you there to stop her and the Geth and Quarian war would have continued unabated without Shephard as peacekeeper. 

I also think the developers were trying to make a point that some things are simply innevitable no matter what you choose to do and no matter how successful you are in what you acheive. 

To me that's what I think the devs were going for and also why it sticks out as such a weird and controversial moment in the trilogy.

The series is nearly completely devoted to cause and effect and even if you screw up, they spent the entire trilogy making your character out to be this absolutely incredible figure that defies all the odds, but at the end of the day he/she is only one human being and can only do so much. I think the ending was supposed to serve as a counter point to the cause and effect nature of the rest of the trilogy where you can defy the odds, you can choose which characters survive and which die, and the Galaxy seems to turn at your whim. After all that, you're meant to feel powerless.

That one ending where it looks like he lives is only viewable if you choose the correct ending and have a score of 5000+, and even then it's not certain. My suspicion with that is they put it in as a kind of nod to the emotional desire players would have had with their version of Shephard, and the need for some people to get the perfect "happy" ending. An easter egg moment for players that completely devoted themselves to getting rid of the Reapers.

*spoilers*

Yes, if you play your cards right.  So, if you played your cards right, and show that peace between synthetics and organics is possible, shouldn't that be reflected in the ending?  That's kind of the whole point of "the shephard" guiding humanity down the right path (or the wrong path).

If you couldn't resolve the war between the Geth and the Quarians, or something like that, then maybe the ending would be fine, and it would make sense that you'd have to choose one of the options.  But, it's incredibly unsatisfying to solve the conflict between synthetics and organics, and then be told a few hours later that you have to make a giant sacrifice to solve the conflict between synthetics and organics.  Whether the starchild is ultimately right or wrong about the conflict being inevitable, from Shepard's,and by extension the player's, point of view, it is nonsensical. 

I don't know what was in the developer's minds, but if they were trying to show that some things are simply inevitable, then that was a poor choice to make. You spend nearly the entirety of the trilogy as the badass who can accomplish anything.  Deciding to change that at literally the last second is poor writing. It doesn't really matter if it was intended or not.  Either it was a bad choice, or bad execution.  Bad either way.

The intention doesn't matter.  If it's my intention to shit on your sofa, and I shit on your sofa, you're not going to congratulate me on the realization of my vision.

You can't spend hours and hours showing on thing then swerve on a dime at the end. It's like if at the end of a Spider-man movie he decides "fuck it, I'm gonna use my powers to get money and get laid".  Or Esmeralda goes "you know what, Quasi really is good deep down and I'm going to marry him and make deformed little babies".  Or if Winston breaks free and leads a successful rebellion at the end of 1984.

If they wanted to do that, then that's shitty writing, and fans were reasonably upset.  You can absolutely have a bleak and depressing ending about how one man is ultimately powerless (again see 1984).  But, if you want to go that route, you have to earn it.  You can't just decide to introduce it at the end.  Readers expect some kind of logic and consistency.   Otherwise it's just a crappy Shamylan twist ending.

Edit:  Plus, *spoilers* they just had Shepard go through the whole doubting himself thing after the fall of Thessia, only to come back with a vengance shortly after, defeat his rival, and save the day.  So, if that was the point they were trying to make, they shouldn't have made the opposite point right before.