Just quick responses, please let me know if there's any clarification needed:
1. Can I have ships gain shields, systems, and change drone fleets as they level
Yes... on some things. There's a min and max mark level for systems, so those can turn on and off. But adding drones or shields is not possible.
Generally speaking, a higher mark ship is a stat boost. The overall design goal is to have variants of things where need be (such as the dire stuff, or other ships that are variants on a base). This is an important distinction from the first game, because in that one a higher-mark ship was literally a new ship. That's not the case here; it's just some numbers moved around.
Now, there IS still that sort of flexibility, but you have to make a descendant type of ship (like the "vicious" stuff that gets extra damage, or the "ensnarer" stuff that gets tractor beams). Those can either be used as special capturables, for certain AIs, OR they can be limited by the mark level of planets so that the smaller ones have a max mark of 3 (for instance) and the larger ones start at mark 4. Then the higher-mark enemy planets get more scary stuff, essentially.
BUT, with those, usually I'd prefer a name change ("Vicious Thingie" rather than just "Thingie") because otherwise it gets super confusing for people looking at the sidebar or other descriptions, etc. When a ship changes nature fundamentally without a name change just because of mark level increases, that gets confusing. Hence why the design is what it is.
Most of what I said above is more relevant to granting the AI new stuff as they have higher-mark planets. But it's not going to convert lower-mark stuff of the player or the AI into a new ship line when they level up a certain amount. I could see us adding a feature like that post-1.0, I don't think it would be too terribly hard. But I do think it would be... strange. I'd rather have players keep their old smaller stuff but capture cool new variants later in the game, rather than having unexpected unforseen changes to their ships as they mark up.
2. Can I have AIP gains tied to leveling
I'm not sure quite what you're asking, but I think the answer is no. Do you mean giving the AI some AIP when the players level up ships via a tech or via EXP? Wow, that would be MEAN.
It would make for some irreversible Bad Stuff That Happens Invisibly When You Do A Thing That's Supposed To Be Good, and that's a major design problem. One example is that I had higher-mark ships costing more energy, but it turns out that people could put themselves into negative energy just by unlocking a tech or even just by fighting and having a fleet auto level up. Bad bad bad, the frustration was palpable for people. So those sorts of mechanics that punish you in any way for tech unlocks or fleet upgrades are things I'm against, since they tend to hit players out of the blue and frustrate them.
If you mean if AIs can get higher mark-stuff at higher AIP levels, that does already happen.
3. Can I make my own assets and tie them to the various marks
Not unless you make a variant ship (see #1). You can make the size of higher marks increase, but visually that's all that can differ between those. Generally speaking, when thinking about something like your "The Last Angel" inspired stuff, I'd see that as being a ship that transforms between styles on certain markers or something.
Fun fact, you could make a hack that does that sort of thing now, since hacks do kind of whatever. And you can frankly make them markless if you want, or assign them the min/max marks you want. But hacking would be the way to go for doing those sorts of upgrades, I'd say.
4. Are there instructions, and poly count/texture size guidelines for importing said assets
I need to set that sort of thing up, because my prior ones are out of date. The shader needs to support instancing, and have that enabled. You can have multiple submeshes, but only one mesh. It needs to be a GameObject with VisualSolomeshShip attached to it. You can set up multiple LODs if you wish, and link those across.
For poly counts... generally speaking it depends on how many of these things are being shown. If it's a rare thing that's only one per game, then I'd say 10-30k polys is okay, but we can't go nuts in general with a lot of ships like that. This would be a true singular hero unit. For ships like that, doing some polygon reduction and having lower poly versions be more like 2.5k to 5k is a good goal. For small and midsize ships for that's a good goal in general.
5. Is there a system like journal entries from AIWC that can be triggered by a fleet leveling up?
Not yet, but soon. Although again I doubt leveling up would be a trigger soon; I'd honestly do this through hacking. All the things you want to do right now would definitely be doable via hacking to "level up" each time.
6. Is it currently possible to implement things like the spire core/spire city building mechanics from AIWC?
You'll have to refresh my memory on exactly what you mean, but I'm assuming you mean basically a third-party faction that builds some structures on its own budget and does... whatever logic in order to place things, etc?
If so: yes, it's way more possible in this game than the first one. Marauders, the Nanocaust, and the Macrophage all have different logic that is based on this sort of thing. It's actually crazy flexible, and you can design factions that are quite complex and have their own style of economy that is all of your own making. Aka dark spire gets energy from certain things that other factions do, and they spend that on new stuff. Macrophage and nanocaust work entirely differently. Etc.
7. Is it possible to give the player more than 3 starting fleets, or 1 starting planet?
Um... hmm, that's a good question. Not in a super modder-friendly way I don't think, not in a basic interface fashion. BUT if you added a new faction (that is perfectly modder friendly) that players could add, then that faction could easily grant players more... anything, frankly. On early init, give the player an adjacent few planets, give them some new goodies in late init give them some ships on said planets, etc.
Some things are limited just because we haven't had time to implement stuff that nobody was planning on using yet, but a lot of things are possible for us to add once we get through the 1.0 polish period. The system is baseline set up for a crazy amount of modding. And frankly, if you find you're re really getting into it and want to have access to add extra modding tools that you then use for your mods, PM me and I can set you up with svn access. Then all things become possible, and you can add more things for others, too. You can also then study my ship assets directly if you so desire. Or email me at chrispark7 at gmail, is even better.
Cheers!
Chris