You need 4000 EMS to avoid Shepard die when picking 'destroy synthetics' option.
I personally think the indoctrination/hallucination theory fits what we saw but we have no way of knowing that Bioware intended it like that or that the 'real ending' (if there is one), will be released as a DLC.
The final options are so 'reaper-like' and presented as 'absolutes' (whatever happened to the notion that just because there are repeating patterns there are also bound to be ever so minute variables that can easily throw the 'repetition' line out the airlock?).
Why must all synthetic life die in order to destroy the Reapers?
That option completely invalidates my Quarian/Geth peace, not to mention EDI's growth as a self-aware AI both of which demonstrate that synthetics don't have to always turn on their creators in an attempt to destroy all organic life (which in a sense is what the Reapers are doing by justifying it through 'preservation in Reaper form for your own protection' - a statement that by itself means little to the organic races that are about to be 'preserved' seeing the death tolls) and all were working together to stop the Reapers.
I can understand what Bioware might have wanted to do, but seriously, the current ending leaves way too many questions into the air riddled with plot holes/inconsistencies that throw everything out of whack.