About Vader's Shuttle, it doesn't disturb me, but I must say that those scenes are pretty useless...
Concerning Boba's voice, I prefer the original voice, but for the sense, Boba having Jango's voice, well, it's pretty understandable, no?

Concerning the shuttle, "disturbing" is exactly the phrase I'd use. To one who is use to the terse delivery of, "Bring my shuttle," the laconic delivery and almost iambic pentameter of, "Alert my Star Destroyer to prepare for my arrival," is disturbing. As is seeing the Death Star II hangar bay and hearing John Williams's score altered. I suppose that if you're not familiar with O-ESB or the score all that may seem perfectly natural, but if you are, it all seems just a bit off. (It's also unnecessary, both for the audience and for Vader. Shouldn't his SD always be prepared for his arrival? What preparations could possibly be necessary, or warranted? Did he expect them to set up a mariachi band in full mess dress to greet him?)

Concerning Boba's voice, it only makes sense if you make certain assumptions about what happened to Boba after Jango died. If he was taken in by other Mandalorians (?) like his father, or clonetroopers, he would've kept his accent. If Boba struck out on his own, the primary influence on his speech patterns would've been the media, which was probably dominated by the Core World accents like Coruscanti and Corellian. Although his Mandalorian accent might not have been lost entirely, it would have been attenuated, and he probably would've suppressed it when speaking to Core Worlders like Vader. I've heard that's what Morrison did when revoicing the OT, trying to blend the original Boba voice with his own.