Why Mass Effect 3's ending was not that bad.

Or rather, why the ending was bad for the reasons people are saying.

Was it not what we were expecting?  Yes.  Did it reflect our choices and actions throughout the series?  No.  Did it adequately cover the themes and concepts that the series had presented, especially those regarding what it means to be alive and the coexistence of organic and synthetic?  Fucking hell no.

That being said, it was not as bad as people are pointing out, at least not all the nit-picky details are.  I'll agree that the 'choices' at the end are lame, the AI in the Citadel doesn't even try to explain anything and just shoves exposition down our throat, which also completely devalues the Reapers as villains or threats, and the lack of influence the player has completely breaks the immersion, and the crucible was a complete deus ex from the beginning.

But some of the details people are picking out are not the problem they're being made out to be.  Having Anderson beat you to the console is not a plot hole, neither is the Illusive Man appearing out of no where.  It's simply narrative convenience.  The writers needed to have a final conflict with the Illusive Man so he was there and Anderson was there to both present a counter argument and to raise the stakes with that shootout.  Personally I would have preferred to have the final encounter with the Illusive Man to have been at his base, maybe then we could have been spared that cheap fight with Leng...God I hated that emo-prick.

The bigger thing people are complaining about is how Joker and the Normandy are shown flying away from the Mass Relay explosion.  Again, this is not a plot-hole so much as convenient for the writers.  They wanted to show the impact of the explosion, and they wanted us to be invested in their fate.  This is the same reason your crew is back on the Normandy.  The character you romance would, presumably, be the one you'd be happiest to see alive.

No, it does not it make sense for the characters to be fleeing the conflict on Earth or for them to appear on the Normandy.  But that's what we have, at least until the alternate ending DLC is available.