HEF is useful is you've got a range advantage - say, HILs or Tachyons (although, with the nerf, Tachyons aren't as powerful anymore - though they still have the best range outside of missiles).
I haven't played with enough ships to try out all of the ship systems, though I don't really see the AI (or myself) using IFed's Titan's Hadron Transporter very much - sure, seeing a 25FP siege carrier teleport around the battlefield is hilarious/terrifying, but you only have three charges (and, from what I can tell, either they don't recharge, or recharge so slowly that I've never noticed).
The AI is also pretty bad with IFed's Mercury's Sensor Drones, for some reason. I once watched my AI-piloted Mercury deploy drones at the beginning of a battle (which is fine), but as soon as it was engaged in an actual shootout, it sent its drones out to free-roam... for them to be destroyed. (The Mercury still won, but still. Way to waste your advantage?) Granted, this is just my observation of a single fight, though I wonder if it was just a fluke, or a regularly occurring thing (which would smell like a bug to me).
Accelerated Ammo Feed is pretty awesome, if you fix Railguns to work with them (Railguns need to be swapped from 0.6 charge-up to 0.6 charge-down; known bug, fixed for the next patch). Only downside is that the IFed Toa tends to cap-out with a load of Railguns firing while under the effects of AAF (which is Working As Intended™, I feel).
-- Griffinhart