I've yet to see any definitive evidence for either argument, I just feel that the sheer ammount of hints for the indoctrination theory makes it unlikely to be a coincidence. If you found something that completely undermines the theory, that'll be evidence enough for me to think that bioware just messed up, so please share.
But are you seriously going to argue that using ambiguity in a good way is impossible? All ambiguity in stories is wrong and a sign of bad writing?
When was the last time an ambiguous ending after being promised answers ended well? Lost sure did go over well didn't it?
The "hints" for indoctrination are all coincidental or game-play elements.
-No one but Shep sees the kid
Colliding Meshes and stuff are already pretty bad, no one acknowledged that Shepard was seeing things either. The kid is obviously used to show Shepards anxiety about Earth and the pressure throughout the game. The dream sequences are him trying to save the kid, nothing else.
-Infinite Ammo Gun
Just a gameplay and animation constraint. You should only have to shoot 5-6 times at most anyway. Why not bring up that my Adept Shepard suddenly has adrenaline rush and can slow down time? It's just a gameplay thing.
-No helmet in space
Again, nothing except gameplay. It wouldn't look too good to have him in singed shit armor with his helmet on. It's just for cool effect. Besides, the wards on the citadel are "exposed" to regular space. I thought it was pretty obvious that it has a regular atmosphere like any other planet. You walk around under open sky just like the end sequence in ME1. Suddenly a giant billion year old space station is fine, but it having breathable air without a ceiling is just going too far.
-Anderson (a good guy) representing the renegade option.
This is just to show the lesser of two evils. Destroying all synthetic life includes sacrificing EDI and the Geth, whereas the paragon option saves them and also stops the Reapers.
Everybody seems to ignore everything that is much more explicit in telling you what happened after that too, after giving in to the reapers they still show him what happens to his friends? Why? No reason at all. And they show him what he wants to see, instead of the error of his ways. If they were actually indoctrinating him, they'd show himi that wiping out all life was the right thing to do.
Why show TIM having indoctrination like control over you when he walks in too? If they did that, and then hinted at it with the wavy lines later on that'd be different. But they explicitly show you what indoctrination looks like. You lose control of your body and you get wavy black lines in your vision.
I also don't get how this makes the ending better, it actually makes it a lot worse. If he gets indoctrinated and all that was just a vision planted in his head, what really happened then?
It all really happened, give it up. Indoctrination theorists just see what they want to see.