One thing that would be nice is to add quantity to the upgrade ship screen.

This way, if you wish to have 5 30% shields, you just need to design one and you can install 5 of them.
This would also put less stress on the overall database as it would remove much of the duplication that is currently required to build a half descent ship.

Maybe, they could just create an "Alliance Fund" where members can donate to and then each member would get a Dailly payout from it. You could even get really fancy with it and give each alliance a planet in the galaxy that can hold this fund, but could also be attacked and raided. This would then require the alliance to put defence ships around this planet.

Adding in search features into items tends to use a fair bit of server resources, so it may slow the game as then people would also want commander search, ranking search etc.

If you want to change up the attack system without making things too difficult to learn or program, then the one thing you can add in would be stacking. By this I mean that you set the order of your fleets. The NPCs would simply randomly stack their fleets as well. Then you will have some people that lead with decoys, some that lead with power ships etc. You would also need to add decoys into the NPC attacks so they could do the same thing.

The other way you can go with it is to put a min % a fleet needs to be of the overall fleet in order to participate in an attack, this would effectively eliminate decoys.

As many people have mentioned, the market is a bit "Too Good" for earning money. I discovered myself that it was much more profitable then missions or attacking. So if you want this to be a trading game with a bit of fighting, then leave the market as is and the game will be dominated by the same people game after game. The variable Idea would work well, however it would require a bit more knowledge and patience from the traders, but again, would be more realistic. The biggest trick in designing the game is to not make any one area dominant over all others as you will just get everyone doing the part that gives the best gains.

Emi could always get real tricky with it and make planets in the galaxy, all that have markets, then you have to physically transport the stuff

I'm thinking that there should be a bit more of an amount closeness. Currently Items are sold in groups of 10,000 and 1,000,000, maybe add in 100,000. Especially if the products change their amount as has recently happened. Many of the larger items were sold in 1,000,000 groups have now changed to 10,000. It would now take 100 sales for someone to unload things they purchased at the larger amounts.

Personnaly, I would just create a random amount generator for CHOAM to buy/sell random amounts between 10,000 and 1,000,000 of all products. This would force people to either specialize in one commodity, or have to force buy and sell products to make up differences. This would also make for more independent sales and all in all, make for a more realistic market situation.