Cubase can also do channel assigment on a note by note basis.
You would never get a legato transition if you went from channel to channel because of the way MIDI works. Data is specific to the channel, and, for better or worse, messages between channels are incommunicado.
Forgive me for bringing this up again, or to come across as patronizing, but after reading this thread I'm still confused about what exactly the issue is with using Vienna Ensemble/Ensemble Pro. I just tried to do exactly what the OP is doing and it worked perfectly. I do almost exactly this every day, but I don't use it to switch articulations; I use it to send data to different channels in a divisi part on a note by note basis. For example, setting up Strings Ensemble on channel 1, then Violins 1 on channel 2, etc. That way I can sketch using a general patch and then just send different notes of my voicings to different channels. Then using Cubase Note Expressions I can actually shape the dynamic of the individual channels within a single MIDI track.
I've also done this within Sibelius.
Vienna Ensemble is a multitimbral host just like Kontakt/Play. The only difference is the tracks are laid out horizontally rather than vertically. From what I can see, the two do exaclty the same thing. Instead of loading Kontakt, just load Vienna Ensemble, not Vienna Instruments.