Okay, here's a few things I would have liked to see (not necessarily as a group, just individual thoughts):
1) I would have liked to see the Pythian prophesy fulfilled. Laura "saw" their home. That negates the prophesy.
2) I would have liked them to look up the word "fossil" or watched the movie Jurrasic Park to figure out the problem with the whole Mitochondrial Mother thing.
3) I would have liked Kara to be a Cylon, the new, 14th model reconstructed by Leoben.
4) Yeah, I would have liked it if a small fleet (tyllium ship, food plant, maybe cloud 9) kept going.
5) I would have liked it if they landed on earth just a hairs breadth before civilization so that they could inject into the ancient mysteries (pyramids, atlantis, stonehenge, etc)
6) I would have preferred if Galactica didn't come back from ramming into a cylon base, but used the last of it's thrusters, instead, to shove it into the black hole.
7) I would have preferred if they took a lesson from Boomer and jumped raptors out of the base from the inside.... repeatedly.
8) I would have liked it if there was "A Plan".

Attempting to shoe-horn in a story about humanity's origins on our planet Earth was a big mistake. It simply went against everything that the series had set in motion in the previous seasons.

The problems with the ending are the result of poor planning earlier in the series.

RDM should have decided from the very beginning what Head-Six and Head-Baltar were and what their purpose was and stuck with that all through (sure, he could have been ambiguous until the reveal, but JMS was consistent with the Shadows and the Vorlons in Babylon 5 from the very beginning before their agendas were revealed at the end of season 3.) Hell, couldn't he have done something radical like identify Head-Six and Head-Baltar as Lords of Kobol from when the Gods lived amongst humans? At least that has some basis in the first and second season!

The "Final Five" storyline and how it dovetailed with the creation of the humanoid Cylons was rather interesting, but it was obviously a retcon and it didn't work at all with the series finale (two Earths with identical constellations in their neighborhood?) Since the series relied so heavily on an ancient backstory, some effort should have been made towards consistency.

The "back to nature" thing at the end was completely out of character for Lee, who was a character always dedicated to doing the right thing on behalf of the greater good despite any self doubts. He just condemned humanity to 145 thousand years of illiteracy and most to poverty for the next 150 thousand. The Lee of only a few episodes ago would never have done that.

It became obvious that RDM had no clue as to "what" Starbuck was after she returned from the dead. She ended up a deus ex machina plot-wise for the whole of Season 4, and her vanishing in the end was just a cheap way out.

It's not so much about how it should have ended as RDM and company should have figured how they intended to end very early on and figured out how they were going to get there while season 1 or 2 was in pre-production.

I've already added one ending on another thread, but this one allows me a few other possibilities, so:

1) Starbuck punches in the coordinates, and the fleet materializes in orbit around Coruscant! She literally has led the fleet to their doom, because in a culture with intergalactic travel, there is no need for the Galactica fleet. All the fleet members are absorbed into the Star Wars universe.

2) The fleet succeeds in rescuing Hera, but Cavil and his cronies are killed in the battle. Anders accesses Cavil's computer network and reports that there is a redoubt that the other Cylons were using for storage of supplies. The fleet jumps there, mortally wounding Galactica in the process. The planet proves habitable, as well as having a number of buildings and good infrastructure. The fleet settles in and begins to reproduce, all the while using the orbiting facilities to begin manufacture of a new fleet for defense. A contest is held to name their new world, and the vote by acclamation is Tera (which is another word for 13; the Twelve colonies of Kobol, plus the Cylons makes thirteen).

3) Raptors jump inside Cavil's fortress and completely overwhelm the defenses using a virus program that turns all the Centurions against Cavil and his people; after the battle it also reloads their primary program with Asimov's Three Laws of Robotics. With the Centurions at their command, various baseships are sent out on scouting missions until a suitable world has been found.

4) Old Earth--home of the Cylons--was not contaminated. The journey to Earth was successful.

5) Cavil's fortress is taken, but in one section a vast array of cryogenic tubes are found; Cavil was preparing to capture all the humans for unknown purposes. Capitalizing on that, the entire fleet enters cryogenic freeze for 500,000 years, after which time the radiation on the Twelve Colonies will have dissipated.

Maybe Kara could have come back instead as Lee's or Sam's "Head-Kara."

9) most of the fleet returns to Kobol in peace (it's also not irradiated) and rebuilds with technology. They carry with them stories of Earth and the lost tribe...

Hmm, the major issue that popped out at me was how easily and apparently without a word of argument everyone gave up technology, and the wasteful way they did it. Adama had a hard time letting go of Galactica, how come everyone else just quietly accepted the (wasteful) loss of every single ship? I would have just left that part out completely and focused more on the characters that didn't get nearly so much conclusion time.

And Cavil blowing his head off - was very unrealistic. That was a guy OBSESSED with survival. Granted, it was kind of awesome..