Consider, we've never seen the Republic's naval officers or their uniforms, only the blue one's Anthony Daniels and Ahmed Best wore in the nightclub scene in AOTC. Chances are, once the Clone Wars broke out the Republic switched to something more militaristic.
Furthermore, it is implied that Dooku delivers the Death Star plans to Palpatine on Coruscant at the end of AOTC. I think Palpatine probably started ultrasecret work on it right away as a means to "combat the Seperatist threat", putting the ambitious Tarkin in charge, which would have given them three years to construct what we saw at the end of ROTS. I think it's completely plausible.
On the other hand, I agree with you totally, Greencapt, that TARKIN should have filled the place of either Mas Amedda or atleast Sly Moore's character. Because, ultimately, what did they add to the story, and why is Darth Vader taking orders from Tarkin in ANH? All of it could have been answered by showing Tarkin as Palpatine's most trusted aide and advisor all along. This is one of the major things that excited me about the possibility of Prequels back in the 80's. But, sadly, Tarkin's story never came to fruition. It's enough to make one weep, or wish for digital effects powerful and convincing enough to paint in Peter Cushing's likeness over the others'.
Just as a sidenote: Mas Amedda never made sense to me. It's quite clear in the OT that Palpatine's regime DID NOT include aliens or women. EVERYONE was Human. Why then, does he always have this alien by his side in the Prequels? And whatever happened to Mas Amedda in the OT, and Sly Moore (a female alien) for that matter?