It may not have been explicitly mentioned in the initial plot outline, but I think it's fairly safe to say that by the way things developed in S1, as many of you have pointed out, Sakai was to go out to explore on the rim, find the Shadows, et al, a la Anna Sheridan. There was a LOT being made of her new mission out on the rim by then. I look at it as when O'Hare went, JMS had to rewrite the angle to fit a character with a pre-existing backstory and couldn't re-hash the same territory on film all over again. The whole mind-rape thing looks like it got transferred to Talia (at least that's my take - the whole copying of her personality to data crystal in late S1 seems to indicate to me that he'd already made that decision), and even THAT had to be shelved when Thompson left the show. And THAT'S what bugs me more than anything else - entire story arc segments we got on film that never saw a resolution due to cast changes, and let's face it, S1 was full of that. I go back and watch that entire exchange between Talia and Kosh and just think, "well this is pointless now."
It just bugs me more in O'Hare's case because a> I loved the character, and b> he was the MAIN character. Not complaining about what we got... Just would have liked to have seen more of Sinclair's story (especially in "In the Beginning," where all we got was a rehash of what we already knew and had already seen). I think I also really liked the chemistry between Sinclair and Garibaldi more than Sheridan and Garibaldi (even if the tension did wind up being the focus for most of S4). And it provided us with more than a few inconsistancies when "The War Without End" came around, too. I loved the episode, mind you, but wow, looking back on it some of the resolutions from B^2 felt forced.
And re: Santiago and Clark. You don't HAVE to mention them by name, because the whole thing reeks of Kennedy and Johnson, and the various conspiracy theories to come out of JFK's assassination. If they were going to go with the whole "VP got off the ship because he claimed he had a virus" argument, then that's just ASKING for us to assume the VP's involvement.