The reason why Phoenix is angry that Edgeworth left (and the reason Edgeworth actually left) differs on whether or not you factor 1-5 into the equation.
In the original (that is, GBA Japanese version), Edgeworth left because he realized that his entire motivation for being a Prosecutor was a lie, that his mentor hated his guts, and that if he didn't leave and find his own reason for prosecuting, he'd merely be going through the motions in the end. Phoenix is angry at Edgeworth leaving because he'd just busted his gut trying to rescue Edgeworth against a man who'd been undefeated for 40 years. (p.s. that's the same basic lesson that Franziska has to learn as well, and any of you who call her character flat - play 2-2 and 3-5 back to back and see for yourself)
With the new case 1-5, Edgeworth's motivations come to light when Gant tells hims that 'He'll know what's needed in the end'. Gant's comparison of himself and von Karma to Edgeworth rattles Edgeworth deeply, because obviously Edgeworth doesn't want to become like either of them. Furthermore, he used forged evidence, even if unknowingly, which means that his convictions are not what they seem, and a lot of the accusations hurled at him would thus bear weight. Edgeworth thus leaves to find out what it means to be a prosecutor, and what he needs to do in order to ensure that he doesn't become like Gant or von Karma. Phoenix, here, is angry because he believes Edgeworth ran away from his responsibilities as a prosecutor instead of facing up to them, not knowing that the reason Edgeworth left is precisely because he needs to properly understand his responsibilities in the first place.
