DQ3 did not go over well with my group, but the character cards for RB2 have been used some. Yes, these characters play differently in the two games, as the mechanics are very different and the attributes of the characters do not match up between the games in any real way. Overall, most of my group prefers characters originally created for RB. The crossover between the games is purely superficial, as DQ at its core is not truly set in Terrinoth by the way it is built (rather that decorated and labeled). Still, some fun is to be had with the extra characters, just don't expect it to really do anything to tie the two games together except in ambiance only.
One thing to look at that has been covered better by others elsewhere are the Mind / Body / Spirit attributes of RB characters ... in that order. Mind is best for the early third of the game. Body is the middle game and the overall balance point. Spirit is needed in the end or often you'll get pulped. Looking at additional characters this way can help you see not only the best tactics for gearing them up but also which ones will have an edge when playing the base endgame or any variants / big box expansions. And yet, when played correctly, I've used a Mind heavy character all the way to end and won.
There is no such comparison in DQ, so therein is another hint to why the characters don't play to the same advantages, one to the next, in both games. DQ characters have attributes that are spread out for equal application throughout the game. There is no way that such and approach between game systems will ever allow perfect crossover between the games.