This may sound kind of weird but I think it's nice that this version of Dr. Frankenstein wasn't an evil man and had taken it upon himself to try protect his creation from Dracula, treating him sort of like a son. Makes his ultimate fate all the sadder though...
Dr. Frankenstein: I could never allow him to be used for such evil.
Dracula: I could. In fact, my brides are insisting on it.
Similarly, his creation holds no animosity toward him. He's distraught when Dracula kills him, and even refers to him as his father when talking to Anna and Helsing.
Van Helsing refuses to kill Frankenstein's creation.
Van Helsing: My work - my job, is to vanquish Evil. I can sense Evil. This thing... Evil may have created it, left its mark on it, but Evil does not rule it, so I cannot kill it.
Anna: I can. *raises pistol*
Van Helsing: *puts pistol down* Not while I'm here.
Carl deciding to go against his orders from Rome to destroy Frankenstein's Monster when it is hanging off a cliff, about to fall, recognising the creature has twice saved his life and deserves a chance.
Frankenstein's Monster: Help me!
Carl: But you're supposed to die!
Frankenstein's Monster: I want to live!
Carl: Alright! Hang on, I'll swing you loose!
Frankenstein's creature's look when Anna thanks him, after he saved her from one of the brides. For someone who has only been treated like a monster or a tool in his life, that thanks meant everything to him, even making him more determined to help the heroes against Dracula.
Future Tear Jerker for all it's worth, but I found it sweet that Van Helsing kissed Anna before they went their separate ways.