Don't shoot the messenger, but since you asked...
It's because Mx costs delta between the two are not insignificant. Bladders, invasive tail horn recurring inspections, unobtanium or seasonally procured gear components, need for "comanche specialty" mechanics to service the latter (if you wish to not pencil whip it that is), it all adds up to the ownership experience beyond just money.
You obviously don't think it's a hindrance, but not everybody feels that way. The Dakota will be much less cantankerous to maintain imo. Every single system of my airplane (Arrow) is cheaper to maintain than in the comanche equivalent.
When we looked at the 250, initially for the incredible discount they carry to the 260B and later, we got to sit in one. The bench seat is really poorly installed in the cabin (tailbone of the bench seat too far forward in the cabin), and robs a lot of effective leg room. It has less leg room than even our arrow. The enclosed luggage area also robs it of additional cabin volume. Both points were non-starters from my wife. I never understood how come an otherwise aerodynamically near-identical and dimensionally identical model would carry such a discount. I figured it out that day.
Other than that, for a 2 person mission, your point is noted. I would go VFR direct to a 250 comanche, at my level of comfort about aircraft ownership. For pax centric ops, it's really not even with the speed advantage. It certainly wouldn't be my first aircraft to own due to the MX nuances, in the way say I wouldn't be uncomfortable about a first-time owning a Dakota, but that metric is irrelevant for the OP in this discussion.