The Pegasus was used as a testbed for a phasing cloak, only half of which is illegal. Why didn't Starfleet continue its phasing research? Just imagine how useful that would have been during the Dominion War.
1) A phased ship that was visible would be useless--it can't fight and it can't be covert.
2) A phased ship that was invisible would annoy the Romulans-perhaps enough to push to side with the Dominion.
3) The Klingons could be given all the jobs where a cloak was needed.
4) Based on the two episodes that I can think of involving a phased cloak (Pegasus and the one where LaForge and Ro were cloaked), I am not sure that Starfleet ever managed to make it truly safe enough to be used for long periods. A device that randomly cloaks individuals seems pretty dangerous to me, as is one that randomly materializes a ship inside a rock or one that can be deactivated with equipment so common its available in Ten Forward.