I guess my take (which coincides with how I was taught) is that it should be preferable to give the patient every opportunity possible to breath for themselves so as to minimize the potential for atrophy of any of the muscles involved in respiration. If I can keep a patient sedated enough so that they are apparently comfortable (as far as I can tell based on vitals and patient activity) but still breathing on their own, I would think that'd be preferable. To me it's similar to giving a patient solu-medrol early during a 911 call. Yes, it's absolutely true that we will never personally see the benefit we gave our patient by giving the solu-medrol early, but it is ultimately beneficial to our patient for a faster recovery.
Yes, this requires more attention on the part of the providers to ensure the patient is tolerating the rate and pressures, but for the transport setting it doesn't have to be that difficult. I am not opposed to A/C 100% and it does have it's uses, but I do try to avoid it if possible.
In our latest protocol update in my critical care gig, we are told to evaluate for post-intubation RASS scores with the ideal score being -2 to -4, which cannot be obtained with paralysis. I'm not sure I agree with keeping someone at -2 (patient awakens with eye opening to voice with positive eye contact, but it's not maintained), and I feel -3 or -4 would be ideal. In that protocol, paralytics are strongly discouraged.