Correct me if I'm wrong, but pulse phasers and Klingon disruptors get to-hit calculations per pulse/bolt, not by the whole volley. As such, they are excellent forward-arc weapons, where you can minimize your angular velocity against the target, and thus get a decent chance of all pulses hitting. They are not as good on side and rear arcs where you are more likely to be using them against a target with a higher AV. Because the Defiant mounts everything forward, it's flight tactics tend toward setting up those low-AV forward shots. Combined with torps, this means the pulse phaser need not load all that fast to be effective. With its shield-piercing chance, it is a superb crunch weapon, especially in combination with quantum torps. The forward-firing optimal configuration means it is probably not the best choice for a 360-degree hardpoint. It is a better idea to mount 2 (or more) of these in forward arcs and use fast-loading beam phasers on the side, rear, and 360 hardpoints.
I've seen plenty of Akiras mount forward pulses combined with a strong beam phaser in the 360 to form a very effective weapons suite with torps. The same goes for Nebulas, Galaxies, and Sovereigns. An Intrepid can also do this to some extent.
All this aside, the pulse phaser hasn't been nerfed, as far as I've seen. It is a knife-fight weapon, as it should be. Realistically (if we can ever say that about Trek), those pulses would degrade over distance and have even less chance of hitting. So, making it a shorter-range weapon fits the DS9 model (I never saw them fired at extreme range -- that's what the torps are for), provides a valid counter-tactic (sabre dancing at range), but maintains the weapon's usefulness. With the longest-ranged torps in the game, Feds can afford to do some sabre dancing, while also having that nasty close-up punch. I still question the shield-bypassing side-effect, since these are supposed to be anti-Borg weapons, and the Borg don't have shields, but I don't think Taldren's going to change that aspect.
Above all, this game should have options and advantages for each race. The Feds have the best options in the game in terms of ship choices, effective weapons, and good defensive systems. They also have the only ships (Excelsior and Nebula) with extreme supplies advantages to the point of being better than larger ships (more shuttles, mines, etc.). In the patch, I have not found pulse phaser-armed ships to be really at all less effective.
Of course, any time a feature is changed post-release, the cries of nerfing or boosting (magic *******) invariably will be heard. It just proves my point that the pulse phaser should have been tweaked prior to release, to avoid just such flame sessions, but so it goes ...