Your other option is a lot better.
In general: if you're going for a heel it should normally look kind of ... dainty, for the lack of a better word.
With flats, you essentially have two options:
a) something that resembles a man's dress shoe in general. This is your alternative and will work with trousers.
b) more of a ballerina style. Will also work with a dress/skirt.
Source: more than a decade in a corporate job and a burning desire to not be killed by my feet. 