Without being able to see your code, it's tough to pinpoint the issue, but I would recommend giving JSON export and import a try. In the three.js source, navigate to utils/exporters/blender and install the JSON exporter (refer to readme.md for instructions). After that, export your model to JSON while carefully selecting exporting options such as geometry type, UVs, and textures. Then, you can bring in your model using the following code snippet:
var loader = new THREE.JSONLoader();
loader.load("model.json", function(geometry, material) {
var m = new THREE.MultiMaterial(material);
var o = new THREE.Mesh(geometry, m);
scene.add(o);
});
I haven't done a direct comparison with OBJ/MTL, but based on my experience, JSON loading is significantly faster than Collada.