^ That's true. In fact Brooks not only starred in Far Beyond the Stars, he directed it - which is the only time in the history of Star Trek that the main character of an episode has also directed it.
The difference is - and I don't want you to think I'm Voyager bashing, I'd do this for any series - there's no point in this episode, it has no effect on future episodes and the chacters don't get to do anything. In Far Beyond the Stars and the Inner Light, Picard and Sisko are both dealing with the situation and Brooks and Stewart are able to take on a different role.
In 11:59, we spend a good 2/3s of the episode watching something that none of the characters ever have any interaction with, while the part is still played by Mulgrew, this doesn't matter because it isn't Mulgrew as Janeway being placed into a different situation, it's just Mulgrew.
If it was a case of aliens who zapped Janeway's brain and made her think she was Shannon O'Donnell I'd be a lot more favourable of this episode - unlike Far Beyond the Stars she doesn't have previous for this - but I'd let it go.
But that doesn't happen. There's nothing Trek about it, and while in The Inner Light, Picard - The Starfleet Captain, Career Oriented - gets to see what it would be like to have a family, which probably goes some way to explaining why his nexus vision is this.
Sisko, who is faltering after the dominion war is taking a turn for the worst, is dropped into the civil rights era, and is shown to see that it is worth fighting the good fight.
There is one thing I can say about all 3, Mulgrew, Brooks and Stewart all give fantastic performances in their episodes. While 11:59 doesn't make sense as a Trek Episode, as a piece of drama, the Shannon O'Donnell plotline is remarkable well done and I did find myself drawn into it.
It's just bad because unlike The Inner Light and Far Beyond the Stars, it doesn't mean anything.
Lets go through the episode:
We start with Neelix asking Janeway about the Great Wall of China and other such early examples of objects that can be seen from space (unlike the Great Wall which can be seen from LEO if you happen to get it on a clear day, but lets ignore that because I didn't know this until researching this).
We then get the set up - Neelix asks Janeway to tell him about the Millenium Gate, and we then see Shannon O'Donnell driving into town (making a Captain's Log, to remind us that this is Star Trek) and meeting the crusty but loveable Henry Janeway and the entirety of Act 1 is taken up by them meeting and falling in love, culminating in a meal by a romantic book. (Which is down right ridiculous, and if you know anything about me, you'd know I like that sort of thing in these cases

)
So then we come to Act 2 and Janeway is using the advanced Stellar Cartography lab...to look at a 3d model of the Millenium Gate, we then get some talk between Janeway and Seven, then we go to the Mess Hall where we get some talk about Seven's Ancestors and such and then we see a holographic picture of Janeway's family that a Ferengi put in a historical database...that Voyager happens to have a copy of...
We then go into Act 3, and there's no set up this time, just back on Earth for the entire act, which culminates in Shannon O'Donnell storming out. In the requisite lover's quarrel.
We then go back to Voyager for more filler, first where we learn about Harry's Uncle Jack and Doc's Uncle Gillette. Then we learn the bombshell - Janeway's ancestor wasn't a martian.
We then cut to the ready room for more filler, back and forth, how will history remember us etc.
Now we're back on Earth, again with no set up and it all turns out happily ever after and the crusty Henry Janeway is convinced to get on with his life and the future turns out the way it should, only this time Biff won't be an insufferable ass.
Then we round off the episode with "Ancestor's Eve" and the origin of the group photo.
The Voyager Crew are incidental in this episode. Most of the episode would still work with little to no changes if it took place on TNG or DS9. (For example the "His cousing was an electric shaver" joke would work equally well if applied to Data). The main story that we're meant to care about is regarding Shannon O'Donnell, but since we're only seeing what happened, and the end is already pre-determined, there's no real tension. No matter what might happen in the episode, since Janeway exists we know it's going to work out for O'Donnell and Janeway in the end.