Hello Stardock,
I think I can point out a couple of issues which would be fundamental for better AI behaviour, more accurate feedback for new players and overall balance.
#1 My primary concern: Missiles
Missile weapons have a tech for +20% attack speed and two components for +25% and +50% respectively (according to tooltips). This adds up to +95% attack speed, which would be alright... if that was how you actually implemented it. You didn't increase the attack speed by 95% but reduced the cooldown by 95%.
So attack speed is 1/cooldown, right? Ok. Lets see what this does:
attack speed [new] = 1/cooldown[new] = 1/(cooldown*(1-95%)) = 1/(0.05*cooldown) = 20/cooldown = 20*attack speed
It added 1900% of attack speed instead of 95%. I am sorry for lecturing you like this, but from these numbers you should see why this is a big issue.
edit: while you are at it, it works the same for kinetics and beams, too, but since it adds up to less then 95% it is less dramatic. But these also get:
+100% attack speed instead of +50% for kinetics and
+81% attack speed instead of +45% for beams with both reducing components
I suspect none of this is intentional.
#2 Jamming
You can stack up jamming to very high values. With only one tullium invested (and about 20 technologies researched, though realisticly more due to need for economy) you can have a fleet of ships with 65% evasion (20% from racial trade, 10% from thalan tech, 10% from normal jammer, 25% from cover-all-fleet-jammer for 1 Tullium). I suspect accuracy of the attacker and evasion of the attacked are additive, so against kinetics you can get: 80%-75% = 5% chance to hit. To an AI this fleet is virtually invincible (or to express it in terms of an equivalent change to hitpoints: +1500%). The only counter is target scanners, which is basicly the same tech.
edit: The Snathi tech tree does not have any accuracy boosting components. There is no way the Snathi tech tree can deal with this efficiently.
(Combine #1 and #2 to build the death star.)
#3 Energy Leech
This is probably a bug, but the component that states: 50% shield piercing does not seem to work. Bema wepaons deployed by a ship I armed with this still did its usual 50% damage to shields and did not harm the ships hitpoints. So it essentially behaved as if the component was not there. The only thing that seems to work is the damage reduction on the smaller variant. But shield piercing is not working.
edit2: This was also addressed with some more details here:
https://forums.galciv3.com/474590
Why should these be addressed?
You could now argue, that I should simply not use these things, since I am spoiling my own experience with this. I wuld counter, that the games stands to gain from rethinking some of these features:
1) I suspect the AI thread assessment does not work based on the explicit attack speed, jamming, targetting values, but rather uses the associated 3 stats, fortitude, value and thread (?). Since you only add a fixed value of threat, it can not account for stacking attack speed boni. Same for Jamming and same for not working Leech.
2) The predictions for the outcome of battles are nice, but for the same reasons as in a) they will deliver inaccurate results. With suggested 65% evasion fleet above I consistantly beat fleets I was "likely to lose" against.
Ok, so we established now, that +20% and -20% are NOT the same thing. Where else is this in the game?
You can get +X% hull capacity or get -X% component mass (hint: the latter one is better suited to make bigger ships). In addition: these values stack multiplicatively with each other. Whether this is unbalanced is debatable however, since you will have way more expensive ships and can't spread them out so well. At 60 logistics your fleets will be close to invincible though. I don't think this should change, I love to build these really big mother ships, this should stay in the game in some way.
That all being said, thanks for the great game. Keep up the good work on it so I can buy some more DLC 
Regards,
zuPloed