Jennifer,
I own 2 Mach 5's: a simplexing unit an a duplexing version, which gives me experience with 3 engines total. The Mach 5 was somewhat of a 'proof of concept' machine which introduced the Memjet technology to envelope printing. The result among users was a love/hate relationship. The good news is that the Mach 6 removes most of the technical impediments and objections, so consider yourself fortunate that you are starting off with a much more viable implementation.
For me, the ability to print 10 x13" now means I can offer a full envelope package when someone orders a #10, 9x12, and 10x13". Previously I would have to print the 10x13 on one of my toner printers. The new adjustable head and table height allows for printing on thick substrates up to a 1/4" or so. I've printed over 250M pieces of 5x8" 21 point board stock without a hitch. (The Mach 5 is limited to light/medium card stock).
The maintenance of the Mach 5 service station is a time consuming, laborious, and dirty process. The Mach 6 servicing is nominal and easy, as you have probably discovered. The recovery time for Mach 5 maintenance cycles is very slow; the 6 recovers in a fraction of the time.
Are you using the job storage feature? For longer runs I save the job to the printer's memory (with a box quantity of 500) and let the operator execute the multiple runs. Easier than sending multiple print commands from Acrobat.
I'd say the Mach 5 still has an application for niche markets, but for general commercial, envelope, and packaging printing the Mach 6 should be your choice.
So all in all, lots of valuable improvements. Good luck with yours!
Dave