Musescore 1.3 - Changing to Different Instrument Within Staff

There are tricks for changing an intrument mid-staf, but these would not change transposition. So you'd better use 2 instruments, fill the appropriate measures with notes, leaving empty the others, place line breaks at the instrument changes and use 'hide empty staves'

The above approach is indeed best in most cases, awkward as it is. I personally do it a different way, mostly so I am not limited to changes at system breaks. Instead, I simple maintain two versions of the sacore - one that sounds right (using Staff Text to effect the change in sound), one that looks right (where I transpose the pitches "manually" via Notes / Transpose). I'm not a heavy user of these sorts of instrument changes, and I don't worry about creating the second version until I'm basically done with the score, so it's not that big a hardship.

I wish I could say 2.0 will address this, but unfortunately, while it will make changing sounds more flexible, it won't address transposition. That's probably the #1 thing I might have wanted to see but won't (it's basically in feature freeze at this point). I'm hopeful it can be addressed soon after 2.0, though.