Hmm... I can't think of what enemy you must have been fighting.... Yuffie's conformer on high lvl enemies would always hit the same or harder then clouds ultima weapon when his hp was full.... and of course alot of times you hp won't be full(sure you'll try to keep it full but it still takes more maintanace then Yuffie's) Also Yuffie's weapon is long range... meaning you can hide in the back row without using a materia slot for the long range materia.
I know against emerald the conformer hit max damage every time. whereas cloud with his Ultima weapon was not(I was in my high 40's or low 50's when I first tried this). Against sephiroth once again Yuffies confomer hit harder.... of course none of my characters ever lost any hp ... so his Ultima weapon was at max power.
In random battles Clouds Ultima weapon would generally hit harder unless his hp started to lower.... and since for most random battles I don't bother healing for every little bit of damage.... his damage abilities drop... and then Yuffie still does more.
Consistency is very important to me... I dont' like having to heal every turn just to keep my attack power up... so generally I keep Cloud with his apocolypse or his Ragnoroc