I also assumed that the crystal would have been used to restore her personality but it still could, assuming that Lyta was programmed by the Vorlons to do this (I don't think for one second that Psi Corp really dissected a loyal agent with stable telekinetic powers). It may even be that Talia's original(?) personality has already been restored and that she is working as a sleeper in Psi Corps.
Takashima was originally to be the traitor but that aspect changed when the actress was unavailable. Thus the baffling scene with Talia and Kosh was great foreshadowing of them tweaking the plot that didn't really amount to much. The only problem then is that Takashima was meant to be the one who knocked out the security to allow the disiguised minbari to poison Kosh in the pilot and that aspect remains unexplained now.
I've heard different things about how the plot would have developed if Talia had stayed. JMS said he planned for Lyta and Talia to appear together in series 3 so I expect Lyta would just have had a few guest appearances with Talia continuing to appear in 7 episodes per season (as it was, Lyta only had two appearances in season 3) before Talia being revealed as the traitor. I wish Andrea had stayed on for another year because I think it would have been better if they'd had the chance to work a bit harder on the love triangle before turning her evil. Andrea was also aware of the possibility of her returning as Bester's assistant, which would have been great fun but for whatever reason (probably scheduling as she left to do regular guest slots on a few other shows like JAG) nothing ever came of it.
If Andrea had been given a few more episodes per season she might have hung on, and her character could certainly have carried more episodes but I don't know how her divorce from Jerry Doyle might have affected her decision (I'm not sure when they split up).
It's possible that Lyta's enhanced powers are supposed to be as a result of Talia's scans. I really liked Lyta being a messenger for the Vorlons and I can see that aspect could have remained hers while all the other plot elements (the rebel telepaths, increasing powers etc) would have been interchangable with Talia.
Then Kosh would have swooped in out of nowhere and deux ex machina'd her back to normalcy with the recording chip. Then Talia would have gone on to be the Vorlon telepathic super weapon that Lyta was in the later seasons.
