Alright. So, further questions:
1. Is it possible to set the number of crews a cap ship uses?
2. Is it possible to set the max levels for a ship? IE, Ship A can have up to 3 levels, while Ship B can have the full 10?
3. Is it possible to have abilities that have more than three levels?
4. Is it possible to set the number of ability points a ship gets per level?
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There may be other ways, I just did what i thought was easiest, and it turned out not quite as easy, 
But anyway, setting Frigates with levels can be done by converting them to Capitals. Now part of the problem is the cap crew requirement and the cap limit on Capitals at 16 ships. Those can be worked around by either adjusting costs of the research for the crews and raising the limit to something else, 48? which is 3 times the normal. Or something very outside, like maybe 200 or so?
When you do this you will have to make them available through the Capital factory, since they are now Capitals, or spawn them. Terraziel was kind enough to show me how, look at fleetbeacon for the Vasari and look at the form.
Frigate Tech AntiFighter
a similar line for a cap should look like:
CapitalShip Tech BattleShip
or whatever.
In the cap factory you can only get 9 slots, that is all there is. But by spawning, you could have as many Capitals as you like and simply create fleetbeaconTech1 with one set of ships, fleetbeaconTech2 with another, it is tedous to convert a frigate to a capital, but use one of the other caps as a model and simply change out the hudicons, smallicons, infocard icons, the picture and mainview icon, the names, unless you want to use the original, and that is easier, is to make a new name and add it to the string file in the string folder. You will want to use the Frigate mesh and the frigate shield mesh in the mesh calls and change out weapon types if that is what you prefer, like something along the lines of the original. The mass should stay at 10000 unless you want to make it heavier or lighter, and the speeds as well, something approximating a cap, or something closer to the original, or even way faster, or slower if that is what you want. In effect take a look at each line as it is in the Frigate entity against the cap entity and adjust as you see best. But the specifics that identify the Frigate need to be in the Cap, if that is your intent, to have a ship that looks like a Frigate, even a giant frigate in a cap form.
Also, if you spawn capitals, you will need to adjust the fleetpoints that the fleetbeacon uses i think the range is 45 min to 60 max. If you add a CapitalScout that uses 50 fleet supply points you will need to add that, so we now have 110. Or you can adjust the cost however you see is best.
In addition you may want to use Newboergs Resize tool, its on the forums, just do a search, to adjust the size of the mesh file for the ship. So your CapitalScout is now twice as large as a normal scout. Make sure to convert the text version of the mesh, if you have the binary you will need to convert to text first. The convertdata for entrenchment and Dekraniks Convert tool or Harpo's is very good at that.
Now, about your questions:
Alright. So, further questions:
1. Is it possible to set the number of crews a cap ship uses?
2. Is it possible to set the max levels for a ship? IE, Ship A can have up to 3 levels, while Ship B can have the full 10?
3. Is it possible to have abilities that have more than three levels?
4. Is it possible to set the number of ability points a ship gets per level?
1. Set the number of crews a cap ship uses? I'm not sure i understand. each ship requires 1 crew, and i believe that is set in the gameplay.constants or the galaxydef file, there is the entity file for the research for the ships as well, which may be exactly where to change it, if it is changeable. I thought, though i could be mistaken, that it was one to one. One crew to one ship.
2. Set the max levels for a ship? This is in the galaxydef file i believe, but im under the impression it is across the board for capitals as a group, not individual ships.
3. Abilities with more than 3 levels? Interesting, this is a nice thought, and i would love to see it, however i have only seen three listed, like the number of weapons per ship, it may be that, that is all we have available to us. But send an email to the devs to ask, they of course know absolutely.
4. Set ability points per ship per level? If you mean, can i level from level 1 to level 2 and get two or three, or whatever points available to me to upgrade several abilities at once with? That i believe is tied to the ship leveling once, from level 1 to level 2, which then grants me 1 ability point to use on whatever ability i want, except the ones locked out until the 6th level i believe. I don't think this is changeable in a file anywhere, but to be honest, haha, i didnt give up when someone told me no it couldnt be done. Usually i went off and asked questions until i found something somewhere that was somehow related to what i wanted. Even round about work arounds that got me only half way there were better than saying it couldnt be done. Haha, Anyway, ask the devs, they are the source here and know much better than any of us.
Although there are some modders out there that are pretty close and have done things the devs maybe didnt think about yet. The one where the guy made a revolving turret around one of the ships using particle forge comes to mind.
Anyway, i hope i have helped somewhat, sorry if my answers are not as definitive as you would like, keep asking and working on it though, you may figure it out, or someone else may and share it with you. That is what makes things so great here.
Take care,
-Teal
