I figured he'd either be an old man or already old and dead when I found him. The question is, what now? Is it just a faction game them? Pick who I want to support between the brotherhood, institute, and railroad and run their missions? Seems like the main quest is over now with no real direction, unless I've missed something.

The game's Central Theme is leaving your old life behind to embrace your new life in the Post-Apocalypse Wasteland and whether or not you can. Shaun represents everything which existed in your old life and if you want to hang onto that then you side with the Institute. The Institute also promises the closest Pre-War existence you can possibly get as well as all of the darker side to it as well.

However, if you've romanced one of your companions, joined the other factions, and so on then you miight believe the Institute is worth fighting against.

Even if it means leaving behind your son who has become the kind of person who kidnapped him.

Make sense?

Wont lie I found it hard to "leave" behind Shaun. Spent the entire game looking for him and when I found him, was very hard to turn my back on him. Course little Synth Shaun I couldnt leave behind no matter how many times I tried to consider it.

I suppose. I had already basically thrown in with the railroad by the time I found him. I'm actually a spy for them. I'm still friendly with all 3 factions (it just occurs to me that maybe Goodneighbor is another faction but I haven't done anything there except what was absolutely necessary for the main quest. I haven't even been back since I did the main quest bit with the dr lady there) so I can go anywhere I want freely. I'm wondering how deep I have to get into the railroad quests before the institute and brotherhood figure out I'm not on their side and turn hostile.