SIGN
Spoilers and whatnot ahead
First of all, the actual ending had some good ideas (using the mass relays to defeat the Reapers was brilliant, for example), but the actual execution was very poor. Shepard's actions themselves aren't necessarily inconsistent, nor are any of the other characters. You're absolutely right about the series being about breaking out of the cycle. But the remaining theme the ending presents goes against the rest of the series. The space god you meet gives you these choices as he explains that the reason this is happening is because organics are doomed to be destroyed by synthetics. This is a statement that it is possible to actively prove wrong during the course of the game by uniting the Quarians and Geth, the latter of which are extremely friendly towards the former after their conflict is resolved. In addition, the main conflict of the series was NEVER about organics vs. synthetics; it was about the Reapers - or some hidden avatar of destruction - versus all of sentient life, including the geth. The geth were used as pawns by the Reapers in both ME1 and ME3, but in the ending they're suddenly lumped in on being on the opposing side. What was the point of introducing Legion in ME2 and being able to give the geth souls in ME3 if they were unequivocally "the enemy" no matter what all along? It's such a blatant turnaround of the themes of the series - the unity of all life organic AND machine in the face of unstoppable destruction. I don't see how you can argue how THAT'S consistent.
There's a bit of inconsistency in the ending options though: even though Shepard, regardless of alignment, just spent the last ten minutes talking to Illusive Man about why controlling the Reapers is an awful idea, TIM's pathway is color-coded blue, for Paragon. Meanwhile, Anderson acts as the proxy for the "destroy" ending, which has been the goal of Paragon and Renegade Shepard for the entire game. And this one is colored red - for Renegade, and now must operate on the flawed principle of the creator gods and destroy ALL synthetic life.
Then there's just the bizarre stuff that doesn't fit at all. Like Joker and your squadmates crash landing on that planet. I'm supposed to believe they just ran away in Shepard's final hour? Plus, no matter what you do, the mass relays are destroyed. So even though you might have cured the Krogan genophage, or got the Quarians their homeworld back, they're all stuck in the Sol system now! The LITERAL deus-ex-machina that appears in the last five minutes, apparently the plan of the ancients all along!....somehow. Stuff like that is what got people upset - the idea that Bioware didn't think out their own endings properly. They were good ideas executed poorly.
*end spoilers*
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You have no time to ponder such questions, as Link has just grabbed a Smash Ball.
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