For Gothita, definitely #43 is better. #44 needs two energies to attack, so that makes #43 much faster. #43 also has some good attacks. The first attack can act as an early nuisance in that induces the defending with auto-sleep. The second attack, while flippy, had the potential to do 40 damage, which isn't too bad.
For Gothorita, both look pretty good. #45 is a fast and a disruptive attacker due to its confusion, while #46 helps discard energies. #45, though, is better in the end. The format focuses on lesser energy attackers, so #46 is not wise to run in a format focusing on minimal energy.
For Cubchoo, run #28. The fact that #29 needs two water energies to attack is a huge letdown, and it really takes away speed already. #28 is more consistent in that the first attack is quite good and needs only 1 energy, and the second attack has a colorless cost.