A purple Crystal ship would be cool. Ive always liked the idea of a Crystal ship that relies on the Crystal vengeance augment. Not sure about that specific loadout though. Don't you actually have to take take damage for Crystal vengeance to work, so the Rock plating might be counter productive. It wouldn't be very difficult to recolor the vanilla ship, but it would be difficult to make it look right. I actually tried creating a purple "Amethyst" Crystal ship, a green "emerald" one, and even a yellow one just the other day.
About CE stuff vs AE stuff:
- I think the Ammo replicator might reduce the usefulness of things like the ammo manufacturer.
- I really think the internal effector should be kept because it works differently than the hacking system. It requires no drone and might possibly be more reliable as it limits system power permanently.
- The on board clone lab would be cool for making new crew still, but I do see how less useful it is compared to the cone system. (Maybe it would be useful to be able to keep you Medbay still? Maybe you could create a crew member after every encounter? Maybe we could add a 4th clone bay power that does the same thing as an on board clone lab?)
- i like the idea of keeping both the AE and CE PDS and having the coexist in harmony.
- The chain weapons seem very interesting, I'm wondering how they would compare to the Auto Lasers?
- The "Swarm" missile launcher in AE is very similar to the already existing Multi-shot missiles in CE, but maybe they will retain some uniqueness because they can be used as single or multi-shot like the chain lasers.
- i hope the Lanius don't overwrite the ghost race! I don't think they would though
A few tiny things I noticed about AE:
- Small graphical updates to the events text screen. What's weird is the rewards screen seems to have a different more solid texture than the rest.
- All of the warnings seem to be in red now, no more white ones.
- The new map and sector screen looks cool
- OMG Two store pages!!!
- Anybody else wonder how manned level 3 doors and sensors would act?
- New explosion animation for missiles, I kind of miss the old one though, I'm so used to it. I feel there will be a place for mods that revert specific things back to vanilla.
- what do you guys think of the new Type C ships? They look like custom mod recolors. I like them, but wasn't expecting those designs.
- Some system icons and status UI icons seem to have been redone and smoothed over. Me like.
Sleeper, do you have any ideas for new weapons or ideas on how current CE weapons could be tweaked etc... To use the new weapon mechanics?
Things I would have liked to see:
I am very surprised that Matthew and Justin said they don't get many requests for new aliens!!! I like that all the aliens they add have their own unique culture though rather than a ton of tiny ones. I could think of a few other races for them to add though. A common suggestion would be plant race, I can see them being pacifists and I can see them healing crew in a room they are in or providing oxygen to that room like the opposite of the Lanius.
I was wishing we could carry more than 3 augments though. A really good suggestion someone had before is 5 augment slots, but some require more than one slot, like a weapon pre-igniter would be 2-3 slots and Adv. FTL Navigation would just be one slot.
I wish there was a way to give blue options depending on what ship you are using, but I guess we don't know they haven't added that yet.
Only 8 sectors still. I was kind of hoping the number of sectors would increase to like 10-12 to extend the game a little bit. I was actually wondering about a "Lite" version of the Infinite add-on that would extend the game just a little bit. Maybe you would have to accumulate 10+ fuel in order to travel to Deep Space rather than the other way around. The only problem would of course be the fact that there is no Crystal sector, but I guess you could get around that the same way the Infinite add on does already with the Ancient Sector. Maybe some non-unique sectors would just send you to deep space anyway, maybe the Ancient Sector could be one of these labeled differently so you don't know it's the Ancient Sector.
Not quite the same as what you suggested, but I still though about it immediately. Player ships isn't really what I'm into. Maybe you should make the ship, as you seem to have figured out the concept already anyway. 
