Since you didn't post images, it's not possible to know for sure, but if you have two of the same species of Pokémon with the same CP but one is a wonder and the other is not likely to make much headway in battle, then they are likely not the same level.
The wonder Pokémon should have less of the semicircle above it filled in compared to the one that's not likely to make much headway in battle. Thus, you should absolutely train up the one that's a wonder.
While they may have the same CP now, they will have a large gap in their CP cap when they are the same level.
Also, it's worth noting that movesets will not influence whether a Pokémon is a wonder or not.