I leveled my engi to 46 when it was the cap, maybe a year ago, quit playing and just returned to the game this week. He is level 47 now. I did a lot of research to test each skill and here is the build I settled on as well as the way I have my skill tabs set up.
Skills:
Wither 6
Leech 6
Empathy 6
Revive 3
Force Shield 0
Suppression 6
Protection 0
Transference 6
Pain 1
Sonic Boom 6
Decay 6
Skill Tab 1
Empathy
Pain
Transference
Sonic Boom
Skill Tab 2
Decay
Wither
Leech (or Suppression - see my note at the very end of this post)
Revive
Note: sometimes when soloing, I will replace Revive with Suppression if I am not have mana regen issues.
I did a lot of research on the defensive and offensive skills. Here are my results.
Both "defensive skills" are worthless: Force Shield, Protection.
The +2 Mana Regen that level 4 Force Shield gives could be useful, but with only 8 spell tab slots, this extra skill will be rarely used if ever. For mana regen, you are better served raising Revive to 3 instead of leaving it at one. The reduced casting cost provides an extra 10 mana per minute. I find I rarely run out of mana even without an implant that provides extra regen. I have one that provides +2 if I need it, but I almost always use one that give me extra damage instead. On the rare occasions I run low, I simply use a stim.
Protection is worthless. At best, maybe it would allow you to take 1 extra hit. At best.
For offensive skills, I calculated the amount of damage they would do in one minute, to make a fair comparison:
1. Decay, 420 damage/min
2. Wither, 300 damage/min
3. Leech, 180 damage/min, plus 180 healing/min
4. Pain, 37.5 damage/min at level 1, plus 150 area damage/min; 97.5 damage/min at level 6, plus 150 area damage/min
5. Transference, 84 area damage/min, plus 96 healing/min
6. Sonic Boom, 42 area damage/min
My most important/favorite skills: Pain is the most effective offensive skill you can have because of the 3 second stun and it only needs 1 point. Transference - there is nothing more beautiful than casting it in the middle of a crowd of hostile mobs and watching every member of your party go from almost dead to full health. Decay - most damaging single target skill, great for bosses.
Lastly, Suppression. I love it because it is the only mez spell in the game. It often is not needed, but it is very nice to have in two situations. First, if you want to solo fast, run into a large crowd of mobs and freeze them all, then pick them off one by one until they unfreeze. Secondly, and probably most important, when your whole team died right underneath a spawn of nasty monsters, run into the middle of the crowd, freeze them all with Suppression, cast a quick Revive, and run back out of range. Note - Unless I have already switched in Suppression because this has happened previously in the same session, this latter tactic does require that I stop and swap out Suppression in place of Leech in my skill tabs.
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