If you're a renegade, Kolyat explains that Thane wasn't praying for himself, he was praying for you. Thought that was really cool, along with the other mentions of your Paragon/Renegade state in ME3.
		
		
	 
oh FFS, I got that response from him. And I imported a 98% paragon save (because of stupid shit in the previous two games giving me renegade points and saving the Rachni queen apparently being Renegade).
Also: third section of TIM was greyed out. I have almost every asset (stupid Kelly got herself killed), full paragon reputation bar, still get bugged. fffff..
On the ending: it feels to me that the extra six months were EA management saying "we want a sequel, make it happen" aka ASUMING DIRECT CONTROL. There is a lot of stuff in ME3 that suggests that this project was time strained, like the journal updating (!) while it doesn't show any updates, store selection having a + sign and so on. The fact that every N7 mission is basically just an MP map with recolored goons from The lair of the shadow broker / Arrival is the other bit. 
They appear to have focused on making choices pan out correctly, instead of checking the overall writing consistency. For instance: the game makes a very, very obvious point about why TIM brought Shepard back and HAD TO bring him back: The Prothean Cypher that exists only within Shepard's mind. But it never states that directly, even going out of its way to claim other, nonsense reasons for why he did it. Even when the beacon on Thessia directly shows this link.
I honestly think Thessia is where the changes begin. Kai Leng was probably just supposed to die on the Citadel, before management went into "GIANT FUCKING SPIDER" mode (for those who know the reference). 
The rush job that is Mass Effect: Deception is further evidence in that direction. There was no reason to turn Kai Leng into a big villain who for some reason should beat Shepard at every turn, until a change was made to change to do so. The Human Reaper for instance, shows up in the IM base for no apparent reason and doesn't do anything. Some of the vids there have no response and are just there to get all 'muahahaha' on you. 
Honestly, that mission and 'boss fight' (that remark about the legs... how would Shepard even know about that?) felt like they were cut and paste from ME2, just to stretch the story a bit and move the citadel one missions later (horizon was pretty much stand alone anyway).
The fact that the art book has a mutated form for TIM, suggests as well that TIM was supposed to be the boss, not Kai Leng. It also makes more sense, since Harbinger would simply be able to repeat Sovereign from ME1, but a little different. 
Basically: TIM shoots himself or you shoot him > ASSUMING DIRECT CONTROL, or having him stand behind you (sans sigaret) when you are lifted upwards. 
No space deity / super AI required, Harbinger simply stating that there is no choice and telling you why the reapers exist, and so on. 
That would have created a lot of minor questions, like why Harbinger wouldn't just destroy the Citadel, but that could have been caught by the 'destroy' ending or other dialogue. Sure, it would have been harder to understand for new players (which is probably why the current endings exist), but it would have been far more satisfying.
The other thing is of course Drew Karpyshyn leaving Bioware right before release of "his" series. Which  should be a rather obvious sign of how and when these things (the changes in story) went down. Assuming it's true, that is.