Metal and Crystal Accumulation: While you naturally need more credits than metal or crystal for purchases, the current ratio is extremely imbalanced. For example, in my latest game I was collecting about 10.3 credits for every 1.4 metal and 1 crystal. This was despite having all possible harvesters and refineries.
How to Fix: Increase the rate at which metal and crystal are harvested. Reducing credit income would slow the game down too much.
Pirate Reinforcements: I hate them. They arrive at random planets at random times, forcing you to constantly sweep your empire for the latest arrivals. They also keep showing up until they've maxed out your supply, meaning you can't build the ships you actually want.
How to Fix: Get rid of the random arrival mechanic. Instead, let us hire them as mercenaries from pirate bases. This would allow us to use pirate ships while allowing us to control when and where they arrive, allong with how many we get.
Rebel Reinforcements: These pose the same problems as Pirate reinforcements: arriving randomly and maxing out supply.
How to Fix: Make them a reward. Have them arrive at planets when we conquered them, representing rebels coming to our aid or the liberated populace joining the fight. This also fits perfectly with the TEC Rebel's style: they replenish their losses by winning their battles.
Auto-Join: Since auto-join is on by default, ships constantly join fleets even if we don't want them to.
How to Fix: Have auto-join default to off. Instead, institute a mechanic for adding ships to existing fleets without having to disband and reform the fleet.
Minor Complaints:
Fleet Icon Colors: You shouldn't have to disband and reform a fleet just because you don't want a hot pink fleet icon (or some other color you don't like).
How to Fix: Allow us to choose the fleet icon's color, or just replace the hot pink one.
No Way to Delete Saves: There is no way to delete saved games we don't want anymore.
How to Fix: Give us a way to delete saved games.
