I get severe lag with ICO as well, much worse than it has been previously.
I've already made comments on diplomatic relations and the Diplomatic Victory!
Mines- as you're aware of from the mines suggestions thread.
Capital ships- there have many threads on how to improve the situation away from carriers-only. Either making carrier capitals as slow as colony capitals or battleships faster would be a basic improvement.
Fighters- currently players tend to build bombers only as fighters are considered ineffective. I've long suggested that it is far more usual for flak to counter bombers. The AM costs for strikecraft could use a rework, they are far too expensive for hangars and non-existent for carrier capitals. Perhaps carrier capitals could pay 50% and hangars and starbases 33%?
The effect of the Deliverence Engine on culture seems minimal, and I've often questioned the mechanic where culture is split among phase lanes as it seems counter-intuitive. A planet with many phase lanes should be an excellent site for culture, yet this mechanic is contrary to that.
I'm not sure what impact trade and refinery ships even have on the game any more, but there are still techs for them. The mechanic in theory is that they can be destroyed for bounty and to cut the income of trade ports and refineries. The issues with them are that I'm not sure that this mechanic still functions; that the ships move too fast; and that they rebuild far too fast, far faster than constructor vessels.
Insurgency is a very poor tech in 1.2- the pirate missions have made it very redundant and it is in need of a major overhaul. Specific techs that could also use work: Martyrdom, Mobile Phase Detection/Degradation, Returning Armada, Ruthlessness, Colony Pods, Resource Focus, Refineries, Vasari Volcanic Population upgrades.
Techs I used to have as in need of work were Planetary Shields which have been boosted in 1.2 by the Novalith rework; Pinpoint Bombardment which was reworked and it is early to judge it; and Communal Labour.
The weapons tech tree has also been a constant subject of mechanic threads, with the worst offender being the Vasari tree because of the positioning of phase missile tech and the low utility of other weapons research.
That's a quick summary, is that what you wanted?