General Confusion:
* Bewilderment
* Disorientation
* Uncertainty
* Perplexity
* Ambiguity
* Mystification
* Puzzlement
* Bafflement
Mental Confusion:
* Discombobulation
* Fogginess
* Muddleheadedness
* Fuzziness
* Clouded thinking
Confusion from multiple choices:
* Dilemma
* Quandary
* Impasse
Confusion caused by deception:
* Deception
* Misdirection
* Misinterpretation
Confusion caused by chaos:
* Chaos
* Disarray
* Disorder
The best synonym will depend on the specific context of your writing.