Hi S.,
I have also had diaper wars with my kids at different times and not every time, but still - diaper wars. Sometimes, my husband and I have to both work to change the diaper because it takes one of us to hold/distract and the other to change/clean.
One thing you may not be able to see is that his skin may be slightly irritated from the poopy and the wipes are burning when you try to wipe it off. A couple things to try - switch brands of wipes or make your own (I've never made my own, but I hear they are much milder than the store bought kind) and use or switch to a different kind of diaper cream. I did not use diaper cream on my kids regularly, only when they needed it. On occasion, my little ones would get irritated though and knew it. The thought of me changing their diaper was pure misery for them and they would get really upset. On a similar note, sometimes the diaper cream burns depending on the kind of rash they may have. My doc suggests mixing Desitin with Maalox (putting it in the fridge is an added bonus). The Maalox is soothing and the Desitin helps it to stick and provides a barrier to the skin.
If there is no rash at all and nothing is irritating him, the only other suggestion I would have is to give him his favorite toy or try to change him near a window so that he can look outside and possibly be distracted. Sometimes that works with my little guy. Good luck!