My sole experience with federations so far was a little wonky. My neighbor invited me to join one, which I did since I knew the end game was coming up. I was a pacifist, and they were pacifist.
So, naturally, they immediately start wanting to declare war on their neighbors, who haven't done anything to hurt anyone.
I declined, and they got miffed. They tried to declare war again, which I declined again, which made them more miffed. Repeat about 4 times, at which point I started letting the requests time out instead of declining immediately. For some reason, that stopped them from gaining more negative opinion on me, but maybe I just hit the cap at -200 for declining war.
They did finally stop asking at that point, and their opinion of me was about to turn negative. Could just be a coincidence that they gave up asking then.
After watching a video on the Star Trek mod for Stellaris, I realized that Stellaris doesn't have any equivalent to the intelligence mechanic from Birth of the Federation, where you could sabotage enemy facilities, ships and populations, or spy on them to steal information. Something like that could be pretty cool, although it could also be very annoying in BotF if you weren't massively better at it than the enemy empires and had it focused on internal security. Having stuff blown up every other turn got old really fast if you didn't.
If they were going to keep the tile system, having intelligence structures would at least give a little more variety. Still, I'm not sure more variety is really the solution to it, since it's really just a shallow system right now. I did get quite tired of dealing with it by the end of the game, since I was usually just slapping research facilities down on almost every free tile, interspersed with the odd power plant or mine just to break up the monotony, and building the odd robot pop for the same reason.