Moore kinda wrote himself into a corner with BSG, setting up a lot of stuff:
- Cylon civil unrest & Final Five
- "One must be worthy of survival"
- importance of Hera as Cylon/Colonial child
- the proverbial flapping of angel wings Tolkien warned us against. The show went from one maybe-maybe not angel in Baltar's head to three angels, with one of them brazenly running around the deck for all to see
- Earth as a promised land
The problem with the ending was - none of it really paid off.
- Final Five were a dud. They couldn't really lead anyone to Earth because their Earth was irradiated hellhole. Their personal tension doesn't really add much to the show where everyone is notoriously at everyone's throat and everyone is highly stressed. And the story they added to out understanding of Cylons didn't amount to anything either. For someone who so sarcastically decried the need to explain background events (Why do Cylons appear every 33 minutes? Fuck you, that's why!), Moore sure invested a lot of time into similarly irrelevant question in Season 4. It doesn't really matter how Cylons made skinjobs. Or how they invented resurrection. Or why they agreed to end the first war.
- "One must be worthy of survival" never amounted to anything. The entire issue was framed in terms of morality vs practicality, acceptance vs vengeance, civility vs barbarity.. Should we force some people to endure hardship (physical, psychological) to keep the fleet running? Should we murder dangerous figures like Cain/rig elections to keep people like Baltar out of power?
But in accordance to ending, none of it mattered. Apparently if you live long enough for designated celestial navigator to give you coordinates to promised land, you are worthy. It doesn't matter whether you are genocidal Cylon with a blood of 25 billion people on your hands or some regular Colonial schmuck who saw his entire civilization destroyed, then spent four years dodging one bullet after the next. You are worthy by the virtue of being here. Conversely, anyone who didn't make it to a transport on New Caprica or had no FTL on Cyrannus was obviously not worthy.
- Hera got shoehorned into a position of prominence, although the reasoning behind it was murky. Why Hera and not any other Colonial child was the proverbial "Eve"? If the answer is once's again "God willed it", then the entire matter loses the stakes. If God is rigging the dice rolls, it's not much of a game.
- Angels, angels everywhere! The problem is of course very much the same - what do characters' decisions matter if God blatantly puts his mighty thumb on the scale? Religious themes are fine, but even Bible used divine interventions more sparingly than late-season BSG.
- Earth wasn't Earth (so not the promised Earth), but it also had humans (so kinda promised Earth). So is it promised Earth or is it not? Are we in the area of grim realism (dictating that there shouldn't be a findable Earth) or mysticism (dictating that there shouldn't be humans on Earth).
Basically all of these things were in contradiction to each other and couldn't really be reconciled in one ending. So in order to make a better ending, the show had to remember what the themes and underlying messages were and stick to them. Adama could die, Roslin could expire, Apollo could never get together with Strabuck (although my personal interest in a private life of a self-destructive alcoholic was pretty much at zero at this point).
Tragedy would be fine, but blatant dissonance was not.
So for a better ending, cut back on angels, don't resurrect Starbuck ("is she a Cylon?" was a worn out card at that point). Cut out the whole arc of God blatantly dragging human to Earth. Make it all about Cylons understanding the enormity of their crimes and trying to come to terms with Colonials. Then Hera becomes relevant again as a visible proof of Colonial/Cylone coexistence. Then the question of being worthy of survival becomes relevant again. And Colonials are not the only ones who have to constantly prove themselves worthy of survival, while genocidal Cylons whistle innocently to the tune of exterminated humans' screams. Then the question of survival becomes a question of morality/civility/reconciliation again. You can even have Earth as something Colonials/Cylons find for themselves rather than being just given one from up high for merely staying long enough in the game.
TL;DR: it would be fine to grind the entire main cast to a paste if the resulting ending actually engages with the major questions posed throughout the series since season one. The dissatisfaction with actual ending stems primarily from the fact that it does not.