I've never quite got the fuss about the ending to ME3. Let's remember exactly what series we're talking about here; Mass Effect, a series with a history of abusing its own canon, plot holes and general poor writing (at least on a large scale... some of the individual characters and moments are good).
ME never was the best written work in history, yes, but it never stooped that low.
Arrival essentially invalidates ME1 (and while as I understand it it was developed by a separate team to the main game, surely there was editorial oversight on the plot?), the Reapers actually making it into the playable galaxy for ME3 also invalidates ME1, the central plot of ME1 is one big hole etc etc.
The arrival of the Reapers does not invalidate ME1 at all; the goal there was to stop them from taking over the Citadel without any warning and cut off the Mass Relay network instantly. We knew the Reapers were coming, eventually; we knew since Sovereign spoke to us, really. The issue was stopping their plan A (instant neutralization of the galaxy) in order to force them into plan B (slowly fly over to old Milky Way and be forced to fight a united galaxy). If anything, ME2 was irrelevant, stopping the collectors from turning colonists into Reaper gelly is far less important than stopping the actual Reapers from eating the whole galaxy. If the Collector Base had been a key asset in ME3, that would have been solved, but alas...
The ending may be one of the most obvious and gregarious examples of this but it only builds on what has come before; a game that collapsed under its own canon (and often quite limited canon at that) and would generally throw up at least one "huh?" moment an hour. If someone cares deeply enough about the plot to be really ticked off by the ending then they would most likely have noticed all the mistakes that came before as well... and surely that would have lowered expectations already.
That's just it; the rather filmsy plot was held together by a pretty interesting and well thought-out universe and memorable characters. Most flaws could be overlooked in favour of this, but since the ending threw these two saving graces away (by having space magic and the Catalyst in the first case, by stranding almost every single important character for no goddamn reason in the second case), we were only left with the atrocious ending this time around. That's why there was so much backlash.
Yes, the ending(s) don't make sense and clearly haven't really been thought through... but then exactly the same could be said for castaways who have been out of contact for years having technology that had only just been developed
Bioware said that was an oversight for gameplay-related concerns. Which is a shame, mind you, a level with very limited ammunition and being forced to use powers/melee attacks would have been great. But compared to the butchering of the universe that the ending is, it's minor.
a ship covered in the (publicly known) insignia of a terrorist organisation being able to dock at the Citadel without anyone batting an eyelid
Did you missed the part where the Council barely accepts to speak with Shepard and only gives him his legitimate Specter status back if he gets lost in the Terminus Systems? Because this is the exact cause for that, apart from the silly Reapers-don't-exist business. Cerberus does love their sigil way too damn much for a covert terrorist organisation, I'll give you that.
why Saren didn't have a few Collector swarms with him when he attacked the Citadel
Because he didn't work with the Collectors, that's all. We know the Collectors and Reapers have them, but not the heretic Geth. Presumably the Reapers wanted to keep the Collectors a secret for now. Remember that the events prior to and during the ending of ME1 happen very fast, there probably was no time for Sovereign to call his Collector buddies to lend him their Swarms. Or maybe no need was seen. Who knows. Again, fairly minor.
why the Reapers didn't just travel from Dark Space without bothering with the Citadel Mass Relay at all considering it only took them (a race of near immortal machines for whom time has no real meaning) a couple of years...
Again, it was clearly stated the goal is to stop them from appearing out of the blue, taking over the Citadel, cutting the Mass Relay network, destroying the political leadership, and routing the Citadel fleet in one swoop. Being forced to travel via conventional means, they must fight for every single planet they want to harvest. ME1 basically saved the galaxy. Not a plot hole at all.
Two elements that were given a pretty high level of importance in ME2 and barely touched on in ME3 were dark energy and the human reaper.
If you remember, a couple of months prior to ME3's release a pretty large amount of stuff was leaked, much of it relating to the plot. Reading that (and between the lines) it appeared that dark energy was going to take the role generic "synthetics" took in the ending of ME3... a threat to the very galaxy itself that the Reapers were designed to prevent. It wasn't gone into in great detail (and I can't remember much of it if it was) but from what I recall the basic idea was that the build up of dark energy would essentially destroy the universe. The Reapers (somehow) prevented this (by destroying nearly all life? I guess I can see how the plot could go). However in observing and interacting with Shepard and humans in general, the Reapers discovered that there was something in human genetic data that could prevent this from occurring. That's why they bothered to build a human Reaper and, as I understand it, the ending choice would have been something along the lines of sacrifice the human race to save the universe (all humans become Reapers... or along those lines) or destroy the Reapers and try to find a different option.
Fan reaction was... well, it's polite to say "mixed" on this... and I can see the team feeling burned with a pretty limited time to think of another option... and so the mess we eventually got was the best compromise they had on what had already been done and what could be (relatively quickly) changed.
Your information is mostly correct, but they didn't react to fan feedback. Mac Walters replaced Drew Kalpyshyn (however you spell his name) as lead writer. It's as simple as that.
Then again, this is Bioware, the team that brought us mages using blood magic in direct view of Templars in DA2 who failed to say a thing... it could just be horrible plotting...
Not the same team. And yes that was horrible, they basically said that they knew it was silly but could not see a way to work around it.
Merging two fundamentally different life forms, in a poorly executed blaze, to create a from one step closer to perfection. How can you not love that idea.
Yeah yeah, sarcasm, I get it. You're too obvious, sorry.