Santiago was assassinated. Clark gained power and started putting his people where he wanted them -- where they could help run things the way he wanted. Clark would have wanted to control B5 himself with less influence held by the Senate Oversight Committee, so I assume his people worked behind the scenes to get the Senators that were strongly a part of that out of office.
Yeah, the Oversight Committee probably got turned into a rubber stamp for Clark's policies, staffed by Senators like the current one we meet in "And Now For a Word," Quantrell.
Plus, Sinclair was a lowly commander, with little evidence that he'd ever had so big of an assignment. He may well have gotten into the habit of checking in fairly regularly. Whereas Sheridan was used to high-profile positions, as he's mostly been in them since the war. Commanding the Agamemnon he learned how to operate independently. He's got lots of confidence. Plus, people probably have more confidence in Sheridan than they did in Sinclair. Sinclair was pressed on them by the Minbari, was a bit suspect, and has never held such a huge command. Sheridan's been highly respected ever since he took out the Black Star.
So combine a more confident and more trusted commander with a weaker senate committee, and that particular background element simply becomes a waste of space.
One detail that *DID* bother me somewhat, is in Season 1 Sinclair was clearly given orders by, not only Hidoshi, but the guy in The Gathering, and I believe 1 other Senator...yet in "Point of no Return" Sheridan in his "chain of command" speech to the locked up Nightwatch guys makes a comment about how a Senator cannot give you a direct order because they are outside the military chain of command.
I can't remember all the "orders" that were given from the various senators to Sinclair, but were the "orders" they gave him more of what an ambassador would do and not what a military commander would do? Perhaps that's how Sinclair drew the line: what he was told fit into what he thought of as his ambassadorial duties and didn't connect much with his military commandering duties, and as such that's why he felt he had to follow the senators' instructions.
Isn't like that man. He mentioned the Senator thing in Season 1, and I just brought up a point that always bothered me. I'm not here to discuss it to death, just that it was an inconsistency that bothered me, thats all...
Yeah, but between us thrashing everything out down to the last frame, plus watching everything a million times, we start picking up on the errors and forgetting the strengths.
I just finished watching Severed Dreams, and all I really noticed were the goofs -- Sheridan hailing the previously-destroyed Roanoake, the cutting in Delenn's speech to the Gray Council because Mira couldn't get the stick to break on cue... sure, I was caught up in the story, but I know the story, by heart. It's the details, most of them goofs, that stick out now.
Ah well. At least Delenn's "Be somewhere else" speech can still stir the heart....
I haven't watched mid-S3 for a while, but I seem to recall that the problem with the Security order was that it came directly from the Ministry of Peace (who are responsible for Nightwatch but not part of the chain of command) - not from the President, or even a Senator, so there is no inconsistency to be explained and JMS didn't "mess up".
Of course, I stand to be corrected if I am remembering it wrongly.
If I remember my season one correctly, the only orders that came from a senator were those of a non-military nature (i.e. how to vote on the Ragesh 3 problem, the dock workers strike). Sinclair could have been getting orders of a military nature from someone that we never saw. And it was a military officer that told Sheridan to take over on B5.