I guess we never really ended up talking about what I would do differently in the commentary. I have in my head an idea for an ultimate Trek story, but that's a miniseries, not a movie, so it is not this.

As for this movie specifically, what would I do differently? Let's take any of the major ideas and rework them:

Our heroes all find their way to the positions we know them in.

If this is what you want your movie to be about, that's fine, though I still don't think it's strictly necessary. You could start the movie with Captain Kirk stepping onto the bridge for the first time and everyone in the audience, fan or not, would be on board (pardon the pun). But to make it work, let more time pass. It's an extraordinary coincidence by itself that all of these specific people end up on the ship at this exact moment in time, which is a different moment in time under entirely different circumstances than in the original continuity. So you have to justify how this exact arrangement of people ended up happening twice under completely different circumstances.

Instead, let the story unfold over a greater time period and you can bring them on bit by bit, lessening that implausibility. The heart of the movie and the relationships is the Kirk-Spock-(McCoy) dynamic. You can still follow that by contriving the two or three of them together early on and letting everyone else come in as time goes on. Does Chekhov really need to be there at the beginning? He's a punchline, really, nothing more. And the others, in terms of serving the plot, aren't much more.

Also, spreading the story out over a greater time period automatically raises the stakes. Say you have Nero and the Narada (or something like them) floating around the edges of explored space for years. But nobody's ever been able to engage or even directly encounter the thing and live to tell the tale. As far as the Federation knows, there's just a big hunk of flying death out there that could strike anywhere at anytime. And they don't know anything about it and they haven't been able to push the frontier out because of it. But now they've got these new state of the art cruiser-explorer ships meant specifically to explore the unknown and able to handle itself no matter what's out there. And who gets the assignment that will end up bringing them face to face with that mysterious floating death? Why, the brash young officer who's been climbing his way through the ranks the past few years (a setup less ludicrous than going from stowaway to captain in six hours), of course. Now you've got this cast of characters we already love facing down something that's been a menace for years or even decades. And, obviously, in the third act, they encounter the floating death just as it's almost ready to launch it's final assault on Earth/Vulcan/the Federation/everybody and have to stop it before it's Too Late.

Original continuity character is stranded in the past.

If this character is coming from an established continuity, then follow the rules of that continuity. Which means that if they know about how time travel works (and, I don't know, HAVE TIME TRAVELED TO FIX THE TIMELINE BEFORE, MULTIPLE TIMES), their actions must be consistent with their actions before. Which means Spock (Old Spock) should in that movie, be endeavoring to fix the damage Nero has done. He also has access to means to both travel further backwards in time and forward again. In this scenario, Old Spock would take any number of actions that follow this general pattern:

(1) Spock finds help.
(2) Spock convinces help that he's from the future and needs to repair damage to the timeline.
(3) Spock, with help, travels to the original point of divergence in the timeline to prevent the damage.
(4) Original timeline is restored, everyone drinks cocoa.

So maybe something like this:

Spock is stranded in the past. He works his way back towards civilization. Presumably if this is a smarter movie, the villain is smart enough to strand Spock somewhere a little more remote than the Federation equivalent of a Chicago suburb. But, he's stranded and he works his way back towards space civilization. He recruits somebody who is willing to believe him, whether it's Kirk, his young self, his father, whoever. He takes a ship and slingshots it around the sun to time travel again, like he's done multiple times before (including once with a death-hangover). Time travel damage repaired, go home, cocoa.

Obviously, this story is not about our young and pretty heroes, so as a movie, it's obviously a no go. But that's fine, since time travel stories are inherently nonsensical anyway and the more time we spend on them, the less they make sense. A bigger problem is that it wrecks the setup of having this new timeline to play in for future movies.

So let's make it interesting. Have Spock legitimately fail and die in any one of these steps. In the original continuity, it's a joke how improbably lucky Kirk and crew get in their travails. At least there it eventually gets lamp shaded - Kirk and crew are legends precisely because their crazy risky schemes always happened to pay off. That's not great story telling, but we can make this story STRONGER precisely by capitalizing on Star Trek's previous story weaknesses. Let Spock try a crazy risky scheme that has a 1 in 100 chance of working. And let the dice roll come up as snake eyes this time, killing him in the process. Then your original continuity character has tried to repair the damage and failed (making his character consistent), which then justifies why this new timeline is different and is going to stay different. You're basically spearing Wash through the chest by doing this, only times a thousand. If you did this, as somebody who has idolized Spock most of his life, I would hate you. But as a storyteller? I couldn't help but be damned impressed.

Future villain comes from the past to wreck things.

Ugh. Fine. But same point with following the rules of the original continuity. If the starting point is the original continuity - then follow those rules. If not, fine, do whatever you want. That's a straight reboot - a straight reimagining and you get free reign to do whatever you want. But original continuity = original continuity rules.

Anyway, you fix this by fixing Nero's motivation. It's weak to the point of being nonsensical. He blames Spock for trying very hard to prevent Romulus from blowing up and failing. How about, instead, now that he's in the past (by purpose or accident), he realizes his home still exists and he has an Awesome Future Ship that can conquer the galaxy. He also probably has the equivalent of Romulus' Grey's Sports Almanac that he can use to become Romulan-Biff. Go home and be Romulan-Biff! Conquer Romulus, become a crazy Emperor and use your awesome flagship to run rampage over the primitive Klingons and Federation! Even if you want to keep the stupid "I must exact revenge on my nemesis by making him watch me blow up his home," do it with the rest of the Romulan Empire at your back!

This idea could stand on its own or just as easily be folded into the first section of this post. The time that has had to pass for our crew to come together was also the time Nero needed to do all the political things he needed to do to become the unquestioned ruler of Romulus. And now, at the start of our story (or the third act, depending on how you're structuring it), he's finally established a solid reign of terror and is ready to steamroll over the rest of the galaxy, starting with Earth and Vulcan. And our hero's have to stop him. Somehow.

The advantage to folding this into the first section is it allows you to have parallel action over years worth of events. Kirk graduates the academy, cut to Nero first arriving in the past and blowing stuff up, cut to Kirk as a junior officer doing something crazy and getting noticed for it, cut to Nero returning home for the first time, cut to Kirk as a first officer clashing with his captain, cut to Nero finally defeating some political rival, and so forth. Whatever the specific events are, the parallel action allows you enormous freedom to cover vast amounts of time while still moving the story at solid clip.

Now, if you gave me a totally clean slate, I'm honestly not sure what I would do (unless you were giving me that miniseries I mentioned), but even starting with the broad strokes of what exists on screen, there are infinite ways to make a story that is both stronger on its own merit and more connected to the source material. Again, I give the filmmakers a lot of leeway because they the writer's strike interfered with their process and they were simply forced to start shooting. In a perfect world, movies wouldn't ever start shooting until the script was ready to go, but by the time that happens, we will have no need for Star Trek because utopia will no longer be science fiction.

Just don't pretend that the story is anything but poor after the fact.

Strong stories arise out of strong situations. 2009 Trek is three half ideas that don't add up to a coherent situation.