Well both the Argo and the Excalibur had the same problem with deus ex machina. The 'shut down after firing the weapon' bit was to keep the big gun from being the solution to every problem and restrict it to the solution to only the problems that nothing else could handle. The Psi-Corp and the other alien governments handling of telepathy was the same thing. At least they tried to handle the problems of the tech rather than sweep it under the rug like some other shows. Not to mention, how would you do a series on 5 or 6 ships all going out to find a cure (or even 2-3)? This is TV, not a book, so the story needs to be restricted to one ship to be able to tell stories in the short time frame of a TV show. Remember, the Rangers were also out looking for a cure and this was mentioned in the series multiple times.
On the issue of jms writing and producing TMoS I want to present the following. Most people like seasons 2-4 of B5 with season 3 seeming to me to be the most popular. Since jms wrote every ep from 'Confessions and Lamentations' (Season 2, ep 18 ) to 'Secrets of the Soul' (Season 5, ep 7) and the vast majority of those are considered some of the best eps, I'll give jms the doubt before worrying about how TMoS will come out.
Here is a list of every ep jms wrote. And don't forget as producer, he was able to insert dialogue as needed to further the arc in eps he didn't write.
Season 1 - 12 eps of 22
Midnight on the Firing Line
Soul Hunter
Infection
The Parliament of Dreams
Mind War
And The Sky Full Of Stars
Signs and Portents
A Voice in the Wilderness part 1
A Voice in the Wilderness part 2
Babylon Squared
The Quality of Mercy
Chrysalis
Season 2 - 15 eps of 22
Points of Departure
Revelations
The Geometry of Shadows
A Race Through Dark Places
The Coming of Shadows
All Alone in the Night
Acts of Sacrifice
Hunter, Prey
And Now For a Word
In the Shadow of Z'ha'dum
Confessions and Lamentations
Divided Loyalties
The Long, Twilight Struggle
Comes the Inquisitor
The Fall of Night
Season 3 - all 22 eps
Matters of Honor
Convictions
A Day in the Strife
Passing Through Gethsemane
Voices of Authority
Dust to Dust
Exogenesis
Messages from Earth
Point of No Return
Severed Dreams
Ceremonies of Light and Dark
Sic Transit Vir
A Late Delivery from Avalon
Ship of Tears
Interludes and Examinations
War Without End, Part One
War Without End, Part Two
Walkabout
Grey 17 Is Missing
And the Rock Cried Out, No Hiding Place
Shadow Dancing
Z'ha'dum
Season 4 - all 22 eps
The Hour of the Wolf
Whatever Happened to Mr. Garibaldi?
The Summoning
Falling Toward Apotheosis
The Long Night
Into the Fire
Epiphanies
The Illusion of Truth
Atonement
Racing Mars
Lines of Communication
Conflicts of Interest
Rumors, Bargains and Lies
Moments of Transition
No Surrender, No Retreat
The Exercise of Vital Powers
The Face of the Enemy
Intersections in Real Time
Between the Darkness and the Light
Endgame
Rising Star
The Deconstruction of Falling Stars
Season 5 - 21 eps of 22
No Compromises
The Very Long Night of Londo Mollari
The Paragon of Animals
A View from the Gallery
Learning Curve
Strange Relations
Secrets of the Soul
A Tragedy of Telepaths
Phoenix Rising
Day of the Dead
The Ragged Edge
The Corps is Mother, The Corps is Father
Meditations on the Abyss
Darkness Ascending
And All My Dreams, Torn Asunder
Movements of Fire and Shadow
The Fall of Centauri Prime
Wheel of Fire
Objects in Motion
Objects at Rest
Sleeping in Light
So 92 of the total 110 eps were written by jms. Yes, some were stinkers, but who is perfect all the time? A lot of those 92 eps are the best the series had to offer, so I'll give jms some slack. B5 tried many new things in Sci-Fi TV, some of which worked and some did not. But they did it on budget and in time, which is part of the reason there is Sci-Fi on TV that is not Trek, IMO.
Also, just to make sure that they aren't any misunderstandings, Season 5 would have largely been the same if PTEN didn't fold at the beginning of Season 4. Jms has said that if the fifth season would have been approved in time, then 'Intersections in Real Time' would have been the season finale of season 4 with the end of the EA civil war finished in the beginning of season 5. If Claudia Christian (Ivanova) would've stayed for season 5, she would have had the Teep arc instead of Lyta. B5 was about the characters during the lead up to the war, fighting the war and the clean up after the war was over. Season 5 was the cleanup after the wars were over. Remember, the duration is a lot longer than the war.
Look at WWII. If you want to see why the war started, then you need to look at hw WWI started and was ended. WWII didn't end after VE and VJ day in 1945. Rebuilding went on well into the 50's and parts of eastern Europe were still damaged as late as 1989 when the Berlin wall fell. So the B5 story didn't end after the Shadows and Vorlons left, but went on with picking up the pieces. I know this isn't how TV usually works, but life doesn't always end 'happily ever after' and I'm glad B5 showed that to me.
Kizarvexis
Sorry for the long rant and I hope I was too windy.