No, you can not get ship unlocking quests with this mod.
I'm working on an AE-compatible update, which won't try to add new events or enemies (hopefully, no enemies with mind control or hacking should appear), but will allow new AE weapons. There may be a few minor changes, some of which are related to new AE modding capabilities, that I don't think I need to mention. I think all that I have left to do is go through the Infinite Space drones and make new Advanced versions of some AE weapons/drones.
Some of the IS drones conflict with some of the new AE drones (Anti-ship Beam II, Fire Beam), so it will take a little longer for me to get done. I don't know yet if I'll just rename them or remove them.
Edit: List of AE Infinite Space advanced tech; I tried to make them similar to the pre-AE ones, which mostly included reduced power cost when it was greater than 2.
- Adv. Repair Bomb - Reduced cooldown
- Adv. Flak Gun - Reduced power cost
- Adv. Swarm Missiles - Increased damage, fire, and breach chance
- Adv. Chain Vulcan - Reduced power cost
- Adv. Chain Ion - Reduced power cost
- Adv. Laser Charger - Reduced power cost
- Adv. Ion Charger - Increased stun chance
- Adv. Stun Bomb - Increased ion damage and stun duration
- Adv. Anti-Combat Drone - Increased fire frequency
- Adv. Shield Overcharger - Reduced power cost
All I have left to do is change some drones, then I can do a quick (and not very thorough) test before I upload it. I hope I can get this done by Friday or Saturday.
I didn't know what to do for the Ion Charger, so I gave it stun chance. I feel that kind of change might be on par with the Hull Beam getting breach chance, although it might not be as useful.
The Swarm Missiles should shoot Artemis missiles with an 8 sec. cooldown (24 sec. total) instead of Leto missiles with a 7 sec. cooldown (21 sec. total), and will have the fire (3) and breach (2) chance that a Hermes missile would have instead of the lower chances that the Artemis has.