So I was in the Institute for the Railroad, was doing Fathers bidding while playing the "i'm not really sure" card. After a few quests (meeting the synth spy, etc), went back to Railroad headquarters and Des told me to seek the help of the minutemen to attack the Institute. Did that. Very difficult battles inside, hardest I have faced in the game, even with high damage combat shotgun and laser rifle. Blow it all up, and decide to try the Brotherhood ending. Interesting side quest about Danse, but no need to reveal that here. Followed the "Autobot" to he CIT and got to the point where i am supposed to jump in the hole in the ground.

Can someone who has done both endings tell me if the battles inside the Institute are pretty much the same fro both the Minutemen and the Brorthehood? Is It worth doing both?t

The battles inside the Institute are pretty much the same.

However, actually getting inside the Institute differes greatly:

For the BOS, you use liberty prime and wreak havoc to reach the institute. LP then lasers a hole into the Institute where you enter.

For the MM, you basically find a hole that the Institute forgot to cover up and enter through there to teleport the rest of the MM in ( )

Basically, all that differs afterwards is whether or not there are BOS or MM in DC and in checkpoints throughout the Commonwealth.