I use the longs tones daily and I spend a lot of time addressing tone quality, speed of air, making sure the middle note has just as much energy as the surrounding note and then I apply those things to the chorales later on. If we have articulation/rhythm issues on a piece of music, I will play through some of the long tone exercises again (not in place of) with said rhythms/articulations in them.
THe warm up sets can be varied with buzzing. For advanced players I have given them a WW book to play some of the scale/chromatic patterns.
With the scale pages: the holy SR keys are done regularly and we eventually play through everything back to back to build endurance.
I think the important thing is that everything you play has to have a purpose and your students need to understand that purpose. Too many students and teacher just go through the warm up without feedback or assessment. Ask students plenty of listening questions: who sounds different? how? what can they do to improve on that?
Hope this helps.