This would fall under "asking for things already denied". If you'd read the OP, then you'd realize that your asking for multithreading, which Sins does not, and as has been stated by the OP, will not support.

2nd

Well if they added a 3rd button row it wouldn't happen and we could add more ships, abilities, ect... So ask for a 3rd button row.

I just want something that is possible now so I can fully test my mod in the dev.exe without being spammed by these popups.

Make an option in game setup menu to select starting positions for players relative to each other. If you select them just relatively galaxy won't be visible pre-game ..... 

And make pirates attack all people that have bounty on them.

Option to reduce fleet supply would be nice as well. (Charge some money for it and once u reduced it you need to research again at normal price to get it back)

I had a similar suggestion on page 2. Hopefully MasonOfSparta see's this...

You want hoshikos, overseers, and dominas to continue auto-casting their heals even when under the effect of armistice, so I don't think we can say "any combat ability" without some qualifiers, unfortunately.

Here is an idea that may or may not be so good, but something nonetheless I'd appreciate seeing...

I'd like there to be a maniple system with fleets, where I can quickly and easily create maniples that all small fleets with all the right ships...

Here is an example...say I have two Halcyons, one Progenitor, 30 illuminators, 6 Iconus Guardians, 6 Domina subjugators, and 12 Aeria's...

Now, what I'd like to do is create three separate fleets...2 fleets will have a Halcyon as a flagship, and one fleet will have the prog as its flagship...each fleet gets 10 illuminators, 4 Aerias, 2 Guardians, and 2 Subjugators...

I'd think it'd be pretty nifty I could just select all those ships and hit the "Maniple" button which would automatically split the ships up into x number of fleets, putting the same number of each ship type in each fleet...

Perhaps even consider a place in the player options where you can create preset fleet formations, compositions, etc...and then you simply click the "Formation 1" or "Composition 1" button and WALLAH! you get your fleet instantly the way you want it...I know that may be a programming nightmare but just an idea...

Here's another idea (sorry if it has already been said)...what if we could have deficit spending...as in like, you que up 10 LRMs even though you only have resources to build say, 4...this would be nice because you probably will have enough resources to build LRM # 5-10 by the time the first four are built...unfortunately, you still have to go back and click the construction que button, forcing you to constantly watch your factory to make sure you use construction time as efficiently as possible...

I'd clarify that I don't want the current construction item to allow you to go into debt...rather, qued items (and let's limit it just to frigate construction) don't require the resources up front...if for whatever reason you don't have the resources at the exact moment a qued item is supposed to be built, then it simply waits until you do have enough resources...

Have the AI have the ability to move it's capital to a better strategic position.

@DirtySanchezz - He wants to make his mod work better in relation to the AI and realizes that not everyone wants to deal with MP.

I do occasioally find my ships following a random trade vessel, and would uasually be amused if it didnt mean I just lost a battle because of it.

That's okay. You put it in such terms that no one noticed.