increase max fleet cap/remove limit completely ?

All it requires is a change to a single line in the gameplay.constants file, but there is not one published mod that does that as it tends to get invalidated with every patch. That said, increasing the fleet supply can have a lot of unintended side effects, from the more obvious lag to the changing behavior of the AI (without a limit the harder AIs will be able to build fleets much larger than most humans can manage).

Further, I advise that the Devs add custom map sharing to Sins of a Solar Empire: Rebellion.

hmm, where would I find that file, and what line would I change ?

In the GameInfo folder of the Sins directory or whatever expansion you play. Do not change that file directory, just copy it. Then go to your mod folder and make a new folder called "Fleet Supply Mod". In that folder make a folder called "GameInfo" and paste the gameplay.constants file in there and open that one in notepad.

While there are tons of gameplay data stored in that file, what you're looking for is this section.

    fleetSupplyData-Small
        fleetSupplyScalar 0.75
    fleetSupplyData-Normal
        fleetSupplyScalar 1.0
    fleetSupplyData-Large
        fleetSupplyScalar 1.25

Basically those numbers are what the default fleet supply numbers (base max 2000) gets multiplied by depending on your fleet size setting. So if you were to change those numbers to 2.0, 3.0, and 4.0, for small fleet supply setting you'd start at 200 supply and your max fleet supply would be 4000. Normal would have a max of 6000, large 8000 etc. You can of course set the numbers as high as you like, but eventually you'll hit a limit to what your computer will be able to handle.

Further, I advise that the Devs add custom map sharing to Sins of a Solar Empire: Rebellion.

Could it be possible to do this with mods? Like with SOA2, or SotF?

Yes as this is very basic and only involves one file.

Yes, but if that mod has a gameplay.constants file in its GameInfo folder, you need to copy and edit that file in your minimod instead of the one from Vanilla Sins. If not then just follow the instructions as normal and activate your minimod above the mod you want to use it with.

Further, I advise that the Devs add custom map sharing to Sins of a Solar Empire: Rebellion.

/me shakes GoaFan77 vigorously and asks... "Oh Magic 8 Ball, Should I bother buying Rebellion?"

    fleetSupplyData-Small
        fleetSupplyScalar 0.75
    fleetSupplyData-Normal
        fleetSupplyScalar 1.0
    fleetSupplyData-FarmAnimal
        fleetSupplyScalar 12.5

massive fleets are like... well... Well, there is a point when it's just ridiculous and actually causes problems.  Be comfortable with normal sized fleets.  The game works better and doesn't lag out or dump you.  Be careful with the period.

Is it possible to do it with Capital ships?

Not on the gameplay.constants file. You will need to modify the regular ship crew research files.

Where can I find these?

In the GamesInfo folder, files RESEARCHSUBJECT_MAXCAPITALSHIPS"___""_" .

So can I some how change the base max from 2000... to like 1000?

Yeah....set the fleetSupplyScalar to 0.5 (50% of the base, which is 2000) for any one of those...just remember which one so you know what fleet supply to pick when you set up the game...