tl;dr:
1) Shepard needs to die because: she was already on borrowed time and the decisions made in order to win meant she did not deserve to live.
2) A 'dark age' is better than a return to the status quo because that was already an 'evil' set up, just less 'evil' than the reapers.
1)I personally feel that Shepard needed to die. The character was all about the struggle, the only person in the galaxy who really understood the threat they faced, and who understood the cost. This Shepard would fight until her dying breath to give the galaxy even a glimmer of hope and an end to the cycle, but she knew she'd never see it. But I think the galaxy ended up with more than hope at the end.
Consider this. Shepard survived ME1, but it would have been totally appropriate, at the end there in the Council Chamber, if she had been killed by that piece of Sovereign. She wasn't, and it was a HUZZAH! moment, but it wouldn't have been wrong for the story. Then, right at the beginning of ME2, Shepard is killed. Then resurrected; but from then on, she is on borrowed time. If you downloaded the SR1 crash site DLC, that's there to make you feel the deaths of the crew, who died while, for some reason, you cheated Death. Then in ME3, pretty much every story you overhear ends in tragedy (PTSD Asari, Londoner trying to patch up soldier, Aethyta, and so on). You can condemn entire species to exctinction - should Shepard survive if the cost was the Krogan's future or the Quarians?
(A number of people have brought up Captian Sheriden of B5, saying he did not die until long after the end of the Shadow War. However, have they forgotten that he already died on Zha'ha'dum? Only to be resurrected by a Deus Ex Machina far more egregious than the Catalyst, who then made clear he was on borrowed time from then on. And who is to say that if JSM had been able to complete his arc as intended, rather than rushing the Shadow War only to get another series, who is to say that the original (artistic!

) intention would have had him dying at the end of the war...?)
2) But, the real reason as to why I feel the endings are hopeful is the fact that the Citadel civilisation as it existed was over. Many see this as a dark age, but it is one where all the species have an equal chance in. Was Citadel civilisation worth saving? The Asari and the Salarians had it sewn up - they'd used the Krogan and then discarded them when it blew back; they turned away the Quarians in their hour of need, however self inflicted, and then looked down on them. They only let the other species play on their terms. At least the Turians were honest about the genophage and didn't pretend to be the good guys. This is implied during the game, where the Salarians are conniving and miss the point totally, and the Asari are complacent and then pay for it. The Turians and Krogan are able to deal honestly and form a truce.
Therefore, from one perspective Citadel civilisation differs from the Reapers only in a matter of scale. The status quo had as much a dismissive attitude as to the rights of the 'lower' species as the reapers did. So doing a Snake Plisken and bringing on a year-Zero situation, to me, is more hopeful than letting the old powers just pick up where they left off.
Also, unlike LoTR and RotJ, ME is rated mature. You don't find that many 'happy endings' in R rated movies. None of the Aliens or Terminator films is really happy. Only Totall Recall and Starship Troopers could be described as happy, and there is a satirical edge to both of those endings.
... I'm gonna predict that Bruce Wayne dies at the end of The Dark Knight Rises and Joseph Gordon-Levitt's character takes over as Batman....