We don't see players complaining about "kicking the AI's ass" via backdoor stuff aka CK II or paradox's other games. It should also make players think twice before entering into a federation noticeably bigger than themselves, without other support. And if you make it extremely hard for the player to achieve there wouldn't be any problem at all.
CK2 is an entirely different genre. You can go from count to emperor of half of Europe and back again in a short time. It won't be anything like that in Stellaris and like in EU4, anti-blobbing is an important concern.
If you want a federation where you're always in control, as Russia with the USSR, you should use vassals as others have said. Federations are not what most people
want them to be, and they're not designed to, they're a group of equals-by-statue and hence each member has an equal right to the leadership. Alliances are far better for those who do not want to give up control, and vassals for those who want subjects they can eventually integrate.
Not to mention that people would riot when their faction is integrated in one war as their federation mate is leader and integrates the other 7 members instantly and wars you for refusal.
Federations are not just another blobbing mechanism, it's not a way to gain (permanent) hard power or to work towards a unified empire, it is not for everyone and it is not for every situation. If made possible to integrate into one faction, it will eventually be too much of a no-brainer mechanism of extreme protection and eventual expansion by unification.
A democratic indirect democracy with many species and sectors is a federation unto itself, after all.