As long as they don't happen too often, and in-between you have spent time properly building the prestige of each title and the champions, and mostly have the matches end without a pin (DQ, draw, time-limit draw, match thrown out, double DQ) then it's a special attraction. You WANT any champion vs. champion match to be a HUGE deal.
From the late-70s - early-90s there were many of these, even inter-promotional matches as World Heavyweight Champions fought each other: NWA vs. WWWF, NWA vs. WWF, UWSA vs. AWA, NWA vs. AWA, NWA vs. UWC, NWA/WCW vs. IWGP, etc... (notice for some reason it was usually involving the NWA)
But as far as intra-promotional nobody did it better than NWA/JCP. They had the World Heavyweight Championship, United States Heavyweight Championship, World Television Championship, and (for a while) National Heavyweight Championship. And in tag-teams the World Tag-Team Championship, United States Tag-Team Championship, and World 6-Man Tag-Team Championship. Yet, at any given time any two singles champions or two sets of tag champions could face each other. It didn't always mean one was pinning the other. But they made them special.
Yes, sometimes one champion did pin the other, and on some occasions one dethroned the other (U.S. Tag Champs Midnight Express and later the Steiners both dethroned World Tag Champs 4-Horsemen and then Freebirds respectively; U.S. Champ Goldberg and later Booker T. both dethroned World Champions Hogan and the Scott Steiner respectively; and #1 contender U.S. Champ Luger beat #2 contender Windham for the vacant World Title).
Of course, in NWA/JCP U.S. singles and tag champs were automatic #1 contenders to the singles and tag World Titles. That's because they booked ALL their titles with IMPORTANCE. It was nothing to see someone bounce between World, U.S., and T.V. Title ranks only to move back up again. They didn't treat U.S. and T.V. titles as "mid-card", but all the title holders were usually main eventers. So moving between titles was no big deal or considered demotions. ANY title could main event a card, a Clash of the Champions, or a PPV.
If WWE would book this way, then yes, I say bring on the Champion vs. Champion matches... even have two tag together at times, too.