Aside from the new skill system, there are issues with how consoles got translated in some cases.
Example: Halon consoles that boosted emitters/hazard changed to boost 'power insulators', which affects shields instead. At the very least, consoles need to affect the same systems.
Additionally, (and related): certain abilities are no longer easy to boost. Hazard Emitters no longer seem to have a console*, and only a single Tier1 skill to enhance them.
My VA HE ability went from 12383 to 9947 hp and 24 to 18 resist with no BO or console changes. Other heals are similar.
*Edit: There is one. But it is the old Biomonitor console.
Comments
*CoughTier2ScientistGroundSkillForSciCaptainsGivesSciTeamIIICough*
I know, that's actually what I was referring to. lol
Basically a crack at the devs for their logic (or lack thereof).