A skillist for these types of characters:

[Mega Man Volnutt]

A witch - I was thinking they'd just be like Black mages. Magic exploiters. I'm also arguing that they'd be able to turn characters into creatures. But I have no idea how to do that so I'll leave that alone.

A Witch hunter - Probably just a warrior


and a cross between a Witch and a cleric (if possible) - Red mage?

 

[Black Pagan]

Here are some things that comes to my mind when i think of a Witch - Affliction Abilities, Curses, Damage over Time, Trapping skills & Evasion Buffs while being Magic damage based.
Here are some things that comes to my mind when i think of a Witch Hunter - Heal over Time, Affliction Immunity Skills & Damage Absorption Barriers while being Physical damage based.

I'm not sure I have ever heard of a cross between a Witch and Mage. I can imagine something like a Tempest - Someone that controls the Passive elements in Nature like Wind Elemental and Lightning Elemental while still being good at Holy Magic or Healing abilities. Maybe you can make the Elements deal Curses, Damage over time and Trapping abilities indirectly, Not the character themselves.

Here are 3 Example Skills that I can think of, for such a Tempest Character :
- A Magical Torrent of Wind that deals Damage over Time to All Enemies, While you get Healed every Turn
- A Wind Barrier that Grants Damage Immunity and Heal over Time to You and Your Allies, While causing a "Fixed" Damage , Every Turn to All Enemies
- A Buff that Boosts your Magic Attack greatly while granting your Normal Attacks Chance to afflict "Cripple".
(A Cripple state would drastically reduce Evasion, Hit-Rate and Crit Chance of an enemy)

 

[gstv87]

Witch:
Blaze, basic Fire, single-target, straight burn damage.
Flame, advanced Fire, single or multiple target, burn & afterburn damage, can be cured with Water or Heal.
Gust, basic Wind, multiple-target, straight wind damage.
Whirlpool, advanced Wind, multiple-target, wind damage and AGI reduction, bonus against Water elemental.
Plasma Vortex, master Fire & Wind, multiple target, burn & afterburn, can't be cured, disintegrates target if HP = 0.

Poison, simple ailment, no straight damage, HP reduction over time, resisted with MDEF.
Disease, advanced ailment, straight HP damage and HP reduction over time, HP damage resisted with MDEF, HP reduction resisted with LUK.
Decay, master ailment, can't be cured except with master Heal spells, dark damage, HP and MP reduction over time, kills target if HP = 0.

Bind, simple derangement, AGI reduction, resisted with MDEF.
Banishment, advanced derangement, resisted with MDEF & LUK, removes target from battle on success.

Conjure Beast, simple invocation, adds an Animal or Beast battler to the user's side.
Conjure Elemental, advanced invocation, adds an Elemental or Magical to the user's side.
Transmutation, master planar magic, turns target into a living creature of similar size, resisted with LVL, MDEF & LUK, restored by master Heal or Major Restoration spells.

 

[kirbwarrior]

Witch - Honestly, I still love the incredibly simple idea I had in VX. The witch gets a skill for each state you wish the player to be able to inflict. Each skill does the same damage (basically a normal attack based on matk). The character is focused on alchemy and targeting enemy's state weaknesses (and this assumes bosses can be weak to them).
Secondary idea is taking the normal Black Mage (like you said) but offer different elements. BM uses the basic Fire, Ice, Lightning? Witch uses Wind, Water, and Darkness. To separate them a bit more, since witches are often thought of as alchemists, then you can give them the trait that makes their item use better. Or they could just be focused around item use and make them fully alchemists.
Lastly, transformation spells could be their forte. "Frog", petrify, Float, etc work great for them in addition to just straight up changing units from doing things like BeDragon to turn an ally into a massive dragon to "Cute Form" that turns an enemy into it's earliest form/palette swap.

Witch Hunter - Just general warrior skills like you mentioned with maybe a splash of Silence, skills that do more damage to summoned creatures, etc. Take the above and make a class that counters it.

Witch/Cleric - Simple is to just combine the above and Cleric skill lists, like you would for a red mage already. To give it the right feel, maybe focusing only on positive effects like healing and BeDragon.
But let's get more complicated. Why would a cleric go to magic? Why would a witch follow and get blessed by a god? Answering those questions would give you a starting spot for skills.

But I have no idea how to do that so I'll leave that alone.

I won't go into much detail (there's better forums for this) but in MV there are some nice plugin makers that can allow this. I don't know if it's possible in vanilla rpg makers to change party members, but it is possible to do it to enemies.

 

[Aesica]

Witch: When I think of a witch, I think of a character that's more about curse/status effects, dots, and stat debuffs rather than straight nukes. Also primarily poison/bio and dark damage. Sample abilities:

• Hex: Chance to apply a multitude of status effects
  
• Evil Eye: Remove x number of positive buffs
• Curse: Reduce stats
  
• Poison: Poison damage to one/all enemies + apply damage over time
  
• Dark ritual: Fully revive a dead character, but sap 20% of their health every round for 5 rounds
• Wither: Dark damage to one/all enemies

Witch Hunter: This brings to mind a class equipped with skills to counter the above--debuff removal, but also anti-mage abilities in either a physical or magical capacity. Kind of like an offensive priest. Sample abilities:

• Esuna: Remove x number of negative status ailments
• Curse Ward: Remove stat debuffs and protect against them for X rounds
  
• Protection from Evil: Reduce dark damage by x%
• Silencing Shot/Strike/Blast/whatever: Physical (or magical) damage + chance to silence the target.
  
• Smite: Light damage to one/all enemies
  
• Draw Magic: Reduce magic damage by a large amount + magical taunt for x rounds (targets caster)

 

[xdan]

A more offensive version of witch hunter:
-Damaged based on the magic damage stat of the target.
-Damage increased by the number of magic skills learned by the target.
-Damage increased by the amount of negative status inflicted on oneself.
-Copy whatever negative statuses have been inflicted upon you and place them into the target (possibly augmented).
-Reduced cooldowns every time a spell is cast on them.

The general rule is "the better the witch is at being a witch, the better I am at killing it". Notice that this design doesn't just remove the actions of the witch like silences or inmunities would, it lets the witch do her thing but takes advantage from it.