Just a couple things I've noticed.. First off, Energetic Pulse Charging as I have pointed out before, still only affects Pulse Guns. Yarlen commented on it and it appears this is not as intended. It is a very simple fix so I'm assuming you guys just forgot about it with bigger issues at hand.
Also, it appears the conversion of Phase Cannons to Phase Missiles (a change that I really hope is temporary and will get changed in 1.0X with some sort of unique weapon mechanic, but in the event that it isn't) was not complete. If they are going to stay this way, fix Desperation. BuffDesperationSelf.entity is still set to apply the AoE buff on PHASECANNON and PULSEWAVE shots, not PM and Wave shots. This too is a simple change, so I'm assuming that the changes to weapon types was last-second and wasn't thought through fully.