Just some random ideas:

• Fighting off a nanobyte invasion
• Aquatic worlds cause rust, which harms production
• A virus causes emotions, which creates chaos (idealogical shifts, political party upheaval, etc.)
• The Iconians create a doomsday device to wipe out all Yor and they have to fend it off
• A faction of Yor friendly to organics breaks off and forms their own civilization
• Fluctuating marketplace prices on some resources could affect them negatively and positively. Maybe they need Prometheus to run their factories and they get a boost in production for low prices and vice versa.
• They could discover a relic like the monolith from 2001 on a planet like Za'ha'dum and worship it like a god.
• With a collective hive mind they could get quest rewards that boost their fleet effectiveness. Colony governors could get boosts too.
• I think it would be neat to have some quest choices blocked off depending on what race you are. Like Yor would be unable to choose an option to save an organic life form. Kind of like quest choices in an RPG.

So in GCIV the Yor create the Borg?

Is it just me or is "hive mind singularity" now as much of a cliche as "rebellious servants" was in the 1990s? We already have the Cybermen and the Borg, and movies such as Avengers: Age of Ultron, and I think the MOO3 iteration of the Meklars may have been a hive mind as well? I don't know what to replace it with but I'm sure there's something new and original to try...

My critique is, why only 1 synthetic species? Or why only 1 major synthetic civilization? You'd think there might be more.

I suggested a new species of synthetic in another thread, but I'll repeat it here. I was thinking that long ago, one civ was facing extinction. In order to survive, they designed machines that could do hard labor and assist their creators. In time their intelligence improved. Once they reached point where they became sentient, they continued their roles as caretakers. The creator species are still doesn't have the population to run a galactic civilization, so the machines do most of the work. As a whole, they are neutral on the good <--> evil scale.

Reminds me of the Slylandro from Star Control 2...

Is it just me or do the Iridium look like they're related to the Iconians?

Also... that sounds like another race from Star Control 2, the Chmrr, which was a fusion of the Chenjesu and the Mmrnmhrmm...

_ a strange electromagnetic waves' melody coming from deep space turns Yorian populations into robotic zombies wasting their time in useless and destructive sexual reproduction simulation. Yor survivors have to find a way to protect themselves from this waves and to  discover and stop the source of this melody. Wich is, in fact, the source of Life through Univers now affecting also evolved synthetic beings. Facing this new information, Yors understand they're no more only synthetic life form but a part of the big whole of Life. Cured of their inforiority feeling herited by the fact to be former iconians' servants, they start to assume vacant galactic peacekeeper role since Thalan disappeared.

Or they just destroy it and so put Life close to the exctinction

It would be cool to see the Yor race citizens more like "programs" or specific task borgs.  Maybe Yor citizens can have excellent bonuses with little to negative consequences.  Maybe a negative would be lack of durantium or whatever resource.  There should be big penalties for acquiring carbon based life citizens since they will likely feel threatened.

The yor should also get the advantage of colonizing extreme worlds but suffer in diplomacy like in usual games.  It could be cool if some of their missions were focused around exterminating races or eliminating all life in certain sectors.  Plays in to the evil borg trope!

More generally, I want the Yor to not feel shoehorned into the game. For instance, don't lock them at 100% approval and make us go to the trouble of manually raising the tax rate to max. Just get rid of those mechanics for any race that's a singular consciousness (biological, mechanical, or otherwise). The way the Yor have been integrated into GC up to this point make them feel like fan additions limited by proper development tools. They're cool as hell and one of my favorite races, but they never feel like they've had the treatment they deserve.

I liked Twin Ping’s idea for a Galactoc Synthetic Games. To me it sounds like a clear cultural path for them. Getting other friendly races to compete in a robotics games of sorts. 

like the real Olympics it could be a large financial burden to the host (planet) for the benefit of cultural boost.  I think there is a good non-‘evil’ quest idea there. 

Expanding on this, perhaps entire separate banks of colonization events that can only happen to carbon, silicon, aquatic, and synthetic lifeforms? A lot of colonization events simply don't make sense for certain races.

The number of unique colonization events wouldn't need to change, per se. Rather, let's say you design 1,000 mechanically unique colonization events, so that all races do have the exact same event table. Many of them could be generic and work for all races (There's a rare resource on this planet! What should we do with it!). However, some of the events could have a decision tree that displays different text based on the player's civilization. Further, you may even make the different versions recognizable across playthroughs. For instance, a 'what to do with these natives' event might offer 'enslave them, learn from them, or leave them alone,' as options to one category of races. But the Yor might instead receive options to 'exterminate them, experiment on them, or leave them alone.'

(Again, not necroing for reason it still aplllies imo as a question)

I'm thinking of this seriously:

How about an "exceed their programming in succesfully re-integrating themselves into galactic society by actually befriending, trading and peacefully co-existing with non Yor?" It all starts with a glitch event that miraculously hacks into their mainframe units and makes a lot them behave like in the aforomentioned scenario which was an existing scenario they had stored and re-run from time to time but always declined to apply in the past. At first they try to destroy the faulty units, then wipe their drives and re-install their initial objectives and finally gradually recognizing there are actual merits in that behavioral pattern after all.