I don't think Shran's addition to cast would've meant removing anybody, at least not right away. Reed was just beginning to get interesting... his conflict with the late Major Hayes over control of security, then his 'Section 31' past in Season 4 worked out well. Sure, Reed mostly came of his shell while being rubbed up the wrong way, but that was a start. I guess as a stiff necked Brit, I've had a soft spot for him since episodes like Silent Enemy and Shuttlepod One.
With the Romulan War right around the corner, some interesting character development could've happened, perhaps even a death amongst the crew.
Shran becoming an Andorian military attaché (or a test to see how Starfleet could work in the future, beginning a crew exchange because of the collation). The Guard no doubt see this as his punishment for losing of his last command.
Reed on covert missions to learn about the enemy, whether behind the lines or back on Earth.
Hoshi trying to decipher messages in code, an unknown new language coming from Romulan ships, uncovering a new race under their control, the Remans. Maybe placed in command during a vital mission or two.
T'Pol having her loyalities tested in two directions - the Vulcans being against war, while uncovering a startling truth about her part Romulan heritage.
Mayweather could receive a promotion, only to be busted back down later to Ensign when he disobeys orders and puts the ship at risk.
Trip presents a significant problem. This could either be ignored entirely, merely showing what happens in his "gap years" or maybe go down the "history books were wrong" route taken by Pocket Books.
Archer's romantic relationship with the Skipper of the NX-02 is tested to the limit during various skirmishes. Meanwhile, Romulan agents are revealed to be behind a disastrous accident within the solar system near Starfleet's shipyards, where Warp 6 trials are underway. This could have a personal connection to the Captain. As a child, he could've witnessed a similar event that nearly killed his father and derailed Starfleet's formation. Evidence that unseen forces have been at work for decades.
Just a few story threads that could be expanded on, giving each character their own arc.