Well, let me try to give you a answer.

1. Cynthia appers multiple times in her gen before the championship battle. At least 4 times.
While Diantha appers in her gen 2 times before the championship battle. Not sure.

2. Most player lose to Cynthia cause she has high level mon and actually good AI. Even players that know what's coming have to stop and grind to be on par with her.
While in gen 6 it's each to get super strong thanks to the new exp share. Which in turns makes the average first time player on par with Diantha, which in turn avoids the whole shock of "she keeps kicking my ass".
Also, Cynthia comes back in gen 5.2 as a surprise super boss that will kick the asses of all trainers that don't know she lives in this one random town house.

3. Cynthia simply has this awesome feeling to her design. Her clothes, her hair, her expression, all of this together makes her very attractive. Plus the whole, "I love a girl that can kick my ass" is a big bonus.
While Diantha's outfit just doesn't have the same magic for most players.

In short.
Cynthia shows up in her game more times which in turn makes her more memorable then being simple the final boss. Her ability to kick the asses of most players that aren't 100% ready for her. And her design.
Makes her just a more enjoyable character.
Not saying Diantha is bad, but Cynthia just better.

Is she's cosplaying as Justice from Helltaker in the picture on the notes?