The "Speed Intensifier" app does not purport to do anything beyond what FakeClockUp does; the animations are sped up, but the speed at which the system runs and apps load is unchanged.
The "Speed Intensifier Add-On" app (which is activated through / requires Winterboard) does purportedly increase the app loading speed by removing the downclock Apple puts in place. The add-on is substantively different than FakeClockUp. The potential sacrifice for the increased speed, however, is decreased battery life in the short term and a shortened expected lifespan for the device.
That is, at least, my understanding.