Alright, been working on a balance mod fairly heavily over the past week or so, chatting in detail about potential changes with several good players. Upon further testing Ant-Ship II is indeed stronger than I gave it credit for - I now consider it is ever so slightly weak, but not nearly as bad as I'd thought.
Keep in mind these are my initial tweaks and while I'm happy with most of them I still have a lot of testing to do. Full list can be found here:
http://pastebin.com/cmWKrurk. For augments specifically, this is where I'm currently at:
Crystal Vengeance Sell Price 40->15 (The Crystal ships are already on the strong end - they don't need 40 free scrap to start with.)
Crystal Vengeance Effect 10%->15% (Meanwhile, the effect is really lackluster; this provides at least a little incentive to keep the augment around rather than selling it at the first opportunity.)
Titanium System Casing Sell Price 50->40
Titanium System Casing Effect 15%->20%
Repair Arm Cost 50->40
Repair Arm Scrap Loss 15%->5% (Scrap amount rounds against you and also costs scrap even when at full health.)
Automated Re-loader Cost 40->60 (Getting cooldowns low enough to get the first volley off is very strong - there's a reason the Pre-igniter costs so much, and in many fights this can serve a similar purpose while also being great in extended fights.)
Shield Charge Booster Effect 15%->20%
FTL Recharge Booster Cost 50->30
FTL Recharge Booster Effect 25%->30% (Upgrading Engines instead of still going to be better in most cases, but this might be cheap & powerful enough to be worth considering sometimes. Potentially most useful for hitting an extra beacon and then fleeing rebels.)
FTL Jammer Effect 100%->200% (Still on the weak side, but now solidly slows an escape. Potentially useful on defense-heavy builds that can't kill ships as quickly.)
Adv. FTL Navigation Cost 60->50
Reverse Ion Field Cost 60->40
Reverse Ion Field Effect 15%->50% (Game says 20% but is actually 15%.)
Reverse Ion Field no longer stacks (Necessary to prevent 100% protection from ion effects.)
Scrap Recovery Arm Cost 50->65
Drone Reactor Booster Effect 25%->80% (Game says 50% but is actually 25%. 100% is the same speed as normal crew.)
Stealth Weapons Cost 50->40
Damaged Stasis Pod Sell Value 15->18 (Reduces the sting of not activating the pod ever so slightly.)