how would you go about doing a conditional check for gender for skills?
That is why I asked for details of what the skills are to do.
There are several tricks that can work depending on what you want the effect to be - your example of "charm" doesn't say the result of the skill.
One option I already mentioned is the one about different elements and elemental damage rates if it is just about damage rates.
If you want to have different states affect the different genders, then the skill should apply two states and each actor or enemy is immune to one of the states but not the other (robots would be immune to both). You'll have to make sure that the text lines for resist are empty as to not give the wrong message in such cases.
No need to have two skills if you are carefull with the skill and state design.
If it is about non-value effects like things on the map reacting differently, you can either check something with event commands or in a few cases even trick the engine by event conditions - for example the hidden items are hidden so that you can add them to the party inventory and reference them with event conditions without the player ever seeing them. So just when the player decides to have a female leader of the party at the beginning (for example) you can add a female token and then have some map events react to it by "item exists" condition.
If everything else fails to be usable, you can call a common event to check anything. In such a case you can
use the build-in meta command to check for a possible gender-tag by script line of a conditional branch if all other options fail (see the help file for the meta command, it automatically reads default notetags, you don't need a plugin to get new notetags done)
EDIT:
Just to add from the other side:
The problem with writing a plugin for this is that neither the plugin nor the plugin writer can read your mind or know what is in your game. So you would still have to give a detailed list of what is to be done when before such a plugin can be written, and then your events would still have to check something in most cases - and that check could easily be done by the existing meta function as well.