It's an iterative series, each game building on the predecessor's mechanics, so there's not any one major twist. But there are a lot of little things that add up. The new movement techniques are great, Salmon Run has been significantly expanded, and just in general the QoL is night and day.
Also, the fact that Ink Armor, Sting Ray, and Main Power Up are not in the game might be the true biggest step forward. S3's meta is in a pretty good spot now.
FWIW, all three Boktai games do have patches if you can't play on original hardware.