...the final story is kind of weak
It really is and I'm not really sure what RTD could have done differently.
Incidentally, I think it was a travesty that there was no 2009 season. We needed more Donna Noble and a bit of River Song story and maybe even another Jenny story?
Every so often, I go to Sylvester McCoy's website to see what sort of things he's come up with. Some of them are right, such as when he said season 5's Companions would be male and female. He just didn't say they would be a couple. Borrowing some of the story ideas from his site that weren't made, here's a made up 2009 Season 5.
2008 Christmas Special - The Next Doctor
Nothing really different except Donna's involved.
501 - Planet of the Dead
Donna instead of Christina whats-her-face. The Doctor and Donna discover that The Swarm comes from a different reality. Donna starts slowly and subtly unraveling.
502 - Scherzo
Inexplicably, time splinters throughout the universe and the Doctor and Donna fall through a crack into another universe with different rules.
503 - Time of the Zygons
The Zygons have taken control of a black hole in the centre of the galaxy. They have been experimenting with time travel and discover how to grow almost anything in a fraction of the time. In minutes they have a Zygon army, ready to take over the galaxy with the help of a zetronic beam. No, I don't know what that is.
504/505 - Fractured Time/Merlin
This one follows on the heels of the Zygon story where the unstable black hole causes ruptures in space time, allowing other universes to bleed through with a risk of the Doctor being sucked into one permanently.
506 - Camelot
There has to be a story about Camelot on a British science fiction/fantasy show, right? Maybe my made up season is getting too much alternate reality stuff going on, but that's where this story is set.
507/508 - Family Reunion/Planet of the Time Lords
The Doctor and Donna join up with Jenny and they all find a world shifted out of phase with the rest of the universe. This world is home to Time Lords who hid there from the Time War and are threatened to be pulled back into "normal" space, where they desperately don't want to go. But, what's causing them to be pulled back into normal space?
509/510 - Medusa Cascade/The Dust of Stars
The ruptures in space time, and the Time Lord planet being pulled into normal space are originating from the Medusa Cascade, where Davros and the remaining few Daleks are trying to escape. The Doctor stabilizes it, trapping the Daleks there once more and putting the Time Lord planet back into its out of phase existence. But, in the process, he loses Donna like what happened at the end of Journey's End. Incidentally, I like this title for some reason. It feels apropos to me that he would lose a star, Donna, and be left with nothing but dust.
I've always thought the Doctor should be in a place, like where Captain Jack is when he meets Alphonso, where he's feeling sad and lonely and meets up with River Song. It's where he tells her about Donna and finding out that she's 2 months away from the expedition to the library, he takes her to Darillium to see the Singing Towers and gives her the sonic. Maybe it's too forced, but I wanted to see that.
511 - The Waters of Mars
This is where there is the break from June to December. This is the time where the Doctor avoids going to the planet of the Ood.
512 - The End of Time Part 1
513 - The End of Time Part 2
I hate the Mickey Smith/Martha Jones pairing. Too forced. They don't belong together.
Anyway, there's my made up 2009 Season 5 that I actually made up just tonight. Probably too much alternate universe/reality stuff in here, but oh well.