Spoilers ahead. You been warned.
It's basically "Join the Templar like bad guys and be as bad as they are" (Join the side that kidnaps children under the pretense of bettering humanity, which is pointless when you surrender it in the process of doing just that) or "Nuke the place and commit murder" with no "play them all against each other/lone wolf/let things play out option.
Basically, you're forced to do bad things either way. I get it, bad things happen that we sometimes can't control, but the options are so limited and there's no "Change mind/walk away" option when you meet Shaun near the end. Why couldn't I have dragged him out of there against his will and force him on life support? Or have been given the option to convince him to not think the ends justify the means and still remain on his side (or not) yet make them take a different approach? I do after all get made leader of it. In that same light why can't I go "Brotherhood is about stopping monsters, mutant or not, it's not just what they are" publicly and replace the elder or get him to see reason? Since, you know, a synth was proven to be beneficial to them.
The exclusion of one or two of these things I might get. But all? Regardless of which faction I join it's always going to be "boom" unless I join the institute. Could have at least knocked them off in different ways while keeping the nuke option. I want more endings and different results. A peaceful approach that is very hard earned after much difficulty. Maybe even "Kill and take over" instead of just destroying. By mole or none mole means.