Hmm. Evil? If psion are allowed, I would try a lawful evil Telepath (for a twist, maybe a Gnome)
The guy might be physically weak, but mentally very strong, and use skills & powers to controll other ones, steadily working on plots how to make himself more powerful... He might even have the Leadership feat, and as a cohort, he could have a psionic warrior...
Stats could be (25 point buy, +4 ability points due to lvl16):
Str8, Dex12, Con12, Int14, Wis12(starting 11), Cha18 (starting with 15), no racial adjustments or equipment modifiers
Equipment:
Belt of Giant Strength +4 (To be able to manifest "Animal Affinty", which, at least as I can see it in the book, is NOT an enhancementbonus)
Glove of Dexterity +4 (to be able to cast Teleport, or IMproved Teleport if "If Thought Could Kills" is allowed"
Amulet of Health +4 or Periapt of Wisdom +4
Ion Stone of ??? (+2 to Constitution or +2 to Wisdom)
Cloak of Charisma +6 (Charisma is now 24)
Consider buying a Mithral Chain Shirt of Moderate Reeinforcement (Ectoplasmic armor will later make the "AC" job, but protecting against criticals, especially from blessed weapons, is very useful. Don`t waste an Armor PRofiency Feat on this...)
Feats:
Power Penetration and Greater Power Penetration
Psionic Focus (Telepathy), Greater Psionic Focus (Telepathy)
(The other 2 Feats as fit, maybe Heighten Power, to increase effectiveness of some Powers, or Extend Power / Quicken Power)
(Save DC against Telepathy Power: 21+power level)
Powers:
"Must Have":
Shield of Prudence, Ectoplasmic Armor, Charm Monster, Conceal Thoughts, Remote View, Negate Psionics, Nondetection, Any Dominate power (the higher level, the better), any Teleport spell.
Damaging Spells: Inflict Pain (allows a Save) or Burning Ray (Ranged Touch Attack, Metacreativity)
(I am not sure if all of these powers can be "discovered", I did it from memory)
"Crisis of Breath" gives a nice darth vader effect...
So far, I made this character like a player character, so, if you want him "more dangerous" against a PC group, the Penetration powers are often unneccessary
Tactics:
Mind Blasting, Charming or Dominating. If his enemies use spells like protection from evil, he will have no negate them to use his best powers. (The Protection spells can block these powers)
If he is low on hitpoints (hey, Teleport Trigger or Contingency could really help here, he could have manifested them from a stone), he should teleport to safety, using nondetection to avoid beeing followed.
Alternatives:
You could try the same with an Enchanter, if you don't want (or can't) use psions.
Other ideas:
A high level Druid, Neutral Evil. He is against technological advancement, and tries to force the people out of the cities, using contagion or similar spells.
Animal Companions:
Maybe a Snake (Giant Constrictor, Viper - the next villain of my group will be a druid with a Giant Constrictor). Consider making it a Dire snake (none out yet, so make her up - I would have done it for my Druid, but the group is only 4th level...).
For combat tactics:
Use snake to constrict or poison enemies. Wild Shape into any dangerous animal (Dire Bear and similar ones). (Import Stats when generating: Wisdom & Constitution).
Mustrum Ridcully