Allow me to prove part of the Mass Effect Indoctrination theory correct, once and for all, using the code from the save game files themselves.

When you make an important decision in mass effect (anything that the game needs to know about from your saves) it adjusts the value of a "flag" in the save game file. You can change any past decision in a save game file by changing the value of these flags (either 0 or 1).

When you finish ME3, you choose from the three endings, denoted END001 (Destroy), END002 (Control) or END003 (Synthesis).

However, looking at the deconstructed code from the saves, only END001, the destroy ending, actually sets any flags.

The code for the endings looks like this:

End001,

PlotIDSet=(20894,19290,19286),

PlotIDClear=(),

PlotInts=((ID=10185,V=26),(ID=10303,V=25)),

PlotCond=())

End002,

PlotIDSet=(),

PlotIDClear=(),

PlotInts=((ID=10202,V=21)),

PlotCond=())

End003,

PlotIDSet=(),

PlotIDClear=(),

PlotInts=((ID=10203,V=22)),

PlotCond=())

So, for the purposes of a save game, your save won't know whether you picked control or synthesis. Obviously I have no idea yet what any of the flags from "Destroy" actually do (they're unused as far as I can tell in ME3 as it stands) but presumably these denote the three EMS levels (1750-2750, 2751-4000, 4000+) at which you can win the war, or are settings for multiple levels of success (did shepard survive? did earth survive? something else?).

However, if the game was really intended to end after the end credits, why would they bother setting a save game flag when there's no more gameplay?

The only logical conclusion is that it was always the plan to include further gameplay content that could only be reached by picking the destroy option.