Well there is other "intelligent anime," but here is a list of some that feature very intelligent lead characters, although not all are into strategy and manipulation. I would also recommend most any Mobile Suit Gundam to you . . . with the exception of the G and SD series. The numbers to the right are my personal ratings of titles.
Akira - 8
Aoi Bungaku Series - 9
Berserk - 9
Blood+ - 9
Bokurano - 8
Code Geass: Hangyaku no Lelouch - 8
Code Geass: Hangyaku no Lelouch R2 - 8
Crying Freeman - 8
Darker than Black: Kuro no Keiyakusha - 9
Death Note - 10
Ergo Proxy - 8
Eureka Seven - 9
Fractale - 9
Fullmetal Alchemist: Brotherhood - 10
Gallery Fake - 9
Gankutsuou - 9
Gasaraki - 8
Ghost in the Shell - 9
Ghost in the Shell 2: Innocence - 9
Ghost in the Shell 2.0 - 9
Ghost in the Shell: Stand Alone Complex - 10
Ghost in the Shell: Stand Alone Complex - Solid State Society - 9
Ghost in the Shell: Stand Alone Complex - The Laughing Man - 9
Ghost in the Shell: Stand Alone Complex 2nd GIG - 10
Ghost in the Shell: Stand Alone Complex 2nd GIG - Individual Eleven - 9
Golgo 13 - 9
Higashi no Eden - 8
Himitsu: Top Secret - 10
Irresponsible Captain Tylor - 8
Kara no Kyoukai 1: Fukan Fuukei - 8
Kaze no Yojimbo - 9
Master Keaton - 9
Mind Game - 8
Monster - 10
Mouryou no Hako - 10
Mugen no Ryvius - 9
Night Head Genesis - 9
Noein: Mou Hitori no Kimi e - 8
Persona: Trinity Soul - 9
RahXephon - 9
Rainbow: Nisha Rokubou no Shichinin - 10
Sci-fi Harry - 8
Senkou no Night Raid - 10
Speed Grapher - 9
Witch Hunter Robin - 9
Yugo the Negotiator - 9
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