Just 3 small ideas, but I think they're nice to have:
1. Derelict after Battles. A nice idea, because you can have "self-made" anomalies. Just use your Survey-Ship to claim that derelict for a small bonus (Ressources, Experience, Hitpoints, new Tech) ... Maybe as an option.
2. Have an option "random respawn anomalies" to do exactly that *g* - spawn each 10 weeks (for example) a few anomalies to discover. I really hate to see your Survey-Ship becomes useless after claiming that last anomaly.
3. Hero-Ships. It would be good to have some "Hero-Ships" (or assign a Hero (Captain, whatever)to a ship like in Haegemonia) to improve its abilities in battle. Maybe +5% Hitpoints or +1 Speed ... whatever. Nice to have.
Last but not least: We really should rething that Hitpoint / Damage-Table. Add a few zeros (instead of hulls with 40 Hitpoints have it increased to 4000 for example - same for weapons), so it would be USEFULL to have a bonus like "+1% Weapons". +1% Weapons is USELESS when using a ship doing only 20 damage - it will not change anything with that bonus.
Same for Armor, Shields and so on... add a few zeros and make minor bonuses more usefull that way.