Ok, I think you're confusing the formation of the United Federation of Planets with vanilla Stellaris Federations (Alliances)...

When the UFP forms, all planets, except the homeworlds of the other members, fall under ther player's control (so Andoria, etc, remain AI controlled)...

Where as when forming an "alliance", which Stellaris calls a Federation, the AI will maintain control of their empire...

Hello Ruin

Thanks for your answer. In fact in the game i did in the past with ST : New Horizon, i just saw that i had control of the ships (didn't checked the homeworld), but personnaly i prefer
to not have all the ships/Planets from AI (perhaps by not forming a federation, but probably i will loose a lot of things that appears in Start Trek if you don't do a federation)

There was a time where forming the United Federation of Planets did give you the other members' warships, IIRC, but I don't think that was intended, or was a design choice that didn't work out as hoped, as it has since been changed, with just a couple of named ships being given instead...

Taking over all but the homeworlds of UFP members is in fact based in canon... When an civilsation joins the UFP they retain the governance of their homeworld, but their other planets nominally fall under the democratic governance of the UFP, which is why you take over all their planets...

By the sound of it, what you want to do is choose the Now is not the time... option when prompted to Form the United Federation of Planets?, and just maintain the basic Federation/Alliance with the original founding members...

This prompt will continue to appear about every 2 in-game years, however, as it's scripted to ensure the player can form the UFP provided at least 3 of the original founders are still in a Federation/Alliance...