1. A method of operation of a navigation system comprising: generating a signal weight with a control unit based on a feature extracted from a user activity; generating an activity model based on the signal weight for representing the feature as a positive weight, representing the signal weight above a weight threshold, or a negative weight, representing the signal weight below the weight threshold, depending on an activity type, a category of interest, or a combination thereof; classifying a user entry newly received, including multiple instances of the feature including the activity type and the category of interest, based on comparing the activity type and the category of interest to each other for identifying the feature with the higher instance of the signal weight to compare with the activity model; and determining a user's intention based on the user entry classified for presenting a point of interest on a device.