a few ideas on how to fix the endings, inspired by indoctrination theory - break for spoiler protection. you know, just in case
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Everything that happens from the moment Shepard gets hit by a beam to the moment when he/she tries to make it to the console inside the citadel after Hackett calls - is real.  its fuzzy becasue Shepard is concussed, wounded, but its still real.

In my interpretation, the actual hallucination doesn't begin until Shepard loses consciousness at the console, after confrontation with Illusive man. and in my interpretation - all 3 choices are valid in their own way... and lead to a different battle once Shepard is woken up by squadmates (if they survive), or hammer reinforcements (if squadmates get hit by a beam and die, due to low EMS)

. I'd have to think a bit further exactly how 3 choices affect both Shepard and the battle, but just like with Quarian and Geth conflict, where we can side with one, other or manage to support both - Shepard should ultimately be able to incorporate the effects of the hallucination choice.

like for example, rough outline:

destroy would just weaken all the reaper forces, without destroying them and it would come down to sheer brute force of the combined war assets to destroy them. strength of assets would determine losses and casualties on the filed, both for the fleets and ground forces. but reapers will be gone forever. the drawback is, while reapers will be destroyed completely, even with weak war assets, casualties would be unavoidable even with the strongest force.

control will make the battle easier by possibly turning reapers on each other, but some would eventually escape into dark space. how many will be determined by strength of the war assets and with max forces it could be possible to destroy them all (or only let Harby escape?)

merge could result in a truce and least amount of casualties... but that would also means that reapers would go back into dark space in full force, and could potentially return in some centuries to continue what they started, if the galaxy decides to violate the terms of the truce.

either way - relays remain operational (with low assets they could be disabled and would need to be repaired. but still - not destroyed). Citadel is completely disabled and potentially severely damaged depending on the amount of assets. Crucible is destroyed upon use.

Shepard can die in destroy and control ending if assets are low (from wounds, since there isn't enough medigel/doctors are unavailable/etc), will always survive in merge. merge is the standstill option, as it saves current cycle and preserves the most lives, but it also keeps full threat of the reapers still standing. Control minimizes the threat but doesn't remove it completely. Destroy removes the threat forever, but more people die to accomplish it.

Shepard's choice inside the hallucination, affects the type of energy crucible discharges and how it affects the reaper forces

how does Harby manage to get to Shepard?  Shepard is NOT indoctrinated.  however, Shepard IS weakened and in a vulnerable state, which makes his/her will weaker and allows Harby access to his/her mind.

and just as an off the wall idea.  allow Shepard a forth option inside the hallucination.  to reject all 3 choices and recognize being manipulated.  this option should be extremely difficult to achieve, would require extreme amounts of meta-gaming through all 3 installments and will allow Shepard to use the crucible to incinerate all the reapers without requiring any more fighting from hammer and sword. Citadel doesn't take any further damage, and crucible while completely depleted and deactivated - is still available for salvage.

Multiplayer should NOT have decisive effect on single player.  all the multiplayer maps are basically N7 missions, so completing multiplayer maps gives the same assets as completing N7 missions.  alternatively - single player could receive credits for each multiplayer wave completed, across all characters.  boost amount of fuel Normandy can hold. increase Shepard's charisma... something that is beneficial yet truly optional unlike galactic readiness currently.