It's actually very simple to implement centering for Isotope (just finished a site that does this to look good on mobile touch devices as well as desktop devices). You just include this bit of code from David DeSandro's repository before the usual Isotope code at the end of this block
<!-- centered layout extension http://isotope.metafizzy.co/ --> 
<script type="text/javascript">
$.Isotope.prototype._getCenteredMasonryColumns = function() {
    this.width = this.element.width();
    var parentWidth = this.element.parent().width();
    var colW = this.options.masonry && this.options.masonry.columnWidth || // i.e. options.masonry && options.masonry.columnWidth
    this.$filteredAtoms.outerWidth(true) || // or use the size of the first item
    parentWidth; // if there's no items, use size of container
    var cols = Math.floor(parentWidth / colW);
    cols = Math.max(cols, 1);
    this.masonry.cols = cols; // i.e. this.masonry.cols = ....
    this.masonry.columnWidth = colW; // i.e. this.masonry.columnWidth = ...
};
$.Isotope.prototype._masonryReset = function() {
    this.masonry = {}; // layout-specific props
    this._getCenteredMasonryColumns(); // FIXME shouldn't have to call this again
    var i = this.masonry.cols;
    this.masonry.colYs = [];
        while (i--) {
        this.masonry.colYs.push(0);
    }
};
$.Isotope.prototype._masonryResizeChanged = function() {
    var prevColCount = this.masonry.cols;
    this._getCenteredMasonryColumns(); // get updated colCount
    return (this.masonry.cols !== prevColCount);
};
$.Isotope.prototype._masonryGetContainerSize = function() {
    var unusedCols = 0,
    i = this.masonry.cols;
        while (--i) { // count unused columns
        if (this.masonry.colYs[i] !== 0) {
            break;
        }
        unusedCols++;
    }
    return {
        height: Math.max.apply(Math, this.masonry.colYs),
        width: (this.masonry.cols - unusedCols) * this.masonry.columnWidth // fit container to columns that have been used;
    };
};
</script>
And then you just set up Isotope as usual
<script type="text/javascript">
$(function() {
    var $container = $('#container');
    // the usual stuff for layouting, sorting, filtering, limiting clicks to zones...
</script>