The reapers have an ability to indoctrinate, basically slow-rate mind control where you don't realize it but you start to see things their way and work for them even if you think you are fighting them. This was shows numerous times with important characters in the first game, and in the last one it looks like Shepherd and The Illusive Man are being put under the influence of indoctrination.
In the final mission you rush this portal that beams you up to the citadel where you can make your choice (destroy the reapers, merge all synthetics and organic life, or attempt to turn the reapers under your control). On your way to the beam you get blasted by a giant laser and almost die. You spend the next sequences limping around and visually impaired.
These three choices represent what various characters tried to do throughout the game while being indoctrinated. Saren (the bad guy in the first game) wanted to merge the reapers with us to make us all stronger. It turned out he was indoctrinated, meaning this idea might have been put in his head rather than it be his idea to begin with.
The Illusive Man was always out to control the reapers and put them under his thumb to make humanity stronger. The reapers used this to their advantage and indoctrinated him as well, making him think he could accomplish this. We were told numerous time though in previous games that this would be impossible, meaning either T.I.M. had something super-special or he was just indoctrinated to think this way and the reapers were still pulling the strings for him. Then there is Shepherd's only real choice, but it's a bad one. Kill all Synthetic life, including the Geth (who he just helped raise into full-sentience and sapience) EDI (who is now a friend AI) and the Reapers.
If you pick Synthesis (which is supposedly the 'good' ending) you effectively choose to be exactly like Saren from the first game. This means that it cannot really be the good ending as you fought against it previously and must only seem like the good ending when compared to the rest. This is something the reapers are already doing as well, so choosing this basically agrees with your enemies.
If you pick control you are effectively choosing to be exactly like The Illusive Man, who failed and was also indoctrinated. The cannot be a good ending either and is an option they wanted T.I.M. to choose under indoctrination.
If you pick destroy you are actually freeing the galaxy and all future generations of species from the reapers, but it's made to be tragic because you're agreeing with the reaper child who just spoke to you in saying that organics and synthetics cannot co-exist and will always end up with Synthetics rebelling against their creators. This simply goes against everything you fought for in all 3 games because you finally get the Geth and Quarians to share the planet and you develop EDI by sharing her growing experience. By choosing this option the reaper makes you think you are destroying all synthetic life. Their purpose was to basically regulate this conflict eternally by storing advanced organic life in reaper form (Sythesis of organic and synthetic life through reaper control).
If you pick either Synthesis or Control, you die in the cut scene. If you have enough points, and completed most of the game and pick Destroy though, you wake up on Earth, barely conscious laying on concrete. Now, this is impossible, and is either a huge gaff in the story (I'll explain) or is a clear indication of something else (which I'll also explain).
The beam portal took us to the citadel, which was orbiting the Earth in space. There is no way you would survive the crash back to earth in a monolithic space station and just wake up on concrete without any wreckage of the many miles-long spacecraft. Again, this is either a terrible oversight or something deliberate.
I think it is a clear indication of something else, namely that after the laser blast you entered an indoctrination-induced hallucination where the reapers attempted to finally control you and convince you not to destroy them (and perhaps work for them). This means that if you pick the good option (Synthesis) you give in to the reapers and they control you. If you pick Control, they have turned you into another Illusive Man and you are also under their control. If you pick Destroy, you would be the first person to ever overcome indoctrination and reject their control and carry on to continue your mission even though it has other bad results.
Basically, if you pick destroy, you wake back up on earth and the whole choice had been the reaper's attempt to control you. This leaves room for Bioware to release a REAL ending in Downloadable content and a far better epilogue, etc. Either that or when Shepherd gasps for breath after rejecting indoctrination, he dies there on Earth and the Reapers win, perpetuating the cycle again and meaning that it is the true end.
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