I'd rather have the Institute be the "good" faction but fear of the unknown would make wastelanders hostile to them at first. You'd need to show the wasteland that they're not too bad. They wouldn't do the stuff they did in F4, they'd be working behind the scenes positively but wastelanders would assume they're causing trouble.
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Deleted member 93956
The Surge does take on almost an equivalent of The Institute and does it so much better. Synths, saving mankind, (actually damn useful) tech development, etics, transhumanism... with several perspectives on all of it.
However I wish the Institute where like they where described in fallout 3. As having powerful settlements and using the sythns to do work and keep the area safe. Otherwise why would zimmerman just go around saying hes from teh Instuite
I agree with @Crni Vuk But no. The problem is there's no question synth are sentient. We should have flaws in their programming. Glitches. Dial it back to like gen 2