Favourite on rail shooter of mine has always been Time Crisis. Including this guy.
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Wild Dog, he's in every game, not always as the final boss, but later as the 2nd last one. Play the first game, and he's a guy with a Mauser who blows himself up at the end. Comes back in 2 and the 2nd last boss, with a gattling gun arm, and then in each following game comes back with even more wacky augments, a missile launcher, a tractor beam and his own side kick as well - Wild Fang. Each time he blows himself up after losing and always comes back in the following game.
Also love how in those games the first one was a single player on rails only, and the canon reason for why that is the agent for the single player games is the only one who is badass enough to do these missions by himself, every other agent gets paired, hence 2 players.
Edit: Also now remember a damn fun boss in Time Crisis 4. It's the boss of the 2nd act. Big guy with a gun, but your NPC captain is fighting him in hand to hand, stopping him from shooting you while you shoot him. The NPC will get knocked away, letting the boss resume shooting you. He uses the captain as a weapon at times during the fight. Cool in concept for an on-rails shooter.
https://youtube.com/watch?v=USgwe5q962Q