...and make them shoot-until-they-stay-still bosses?

Maybe the original puzzle should do some extra damage or something...

I don't think such mods exist. If bosses bother you that much cheats are one option...

By the way, is it some specific boss you don't like?

Some time ago I started this game and I loved it. It is a shooter which focus on what it matters, that is of course shooting.

But I stopped playing at the Swamp Monster when I understood what I was supposed to do to win. I was playing Nightmare without any problem until that level, so I think it is not a matter of difficulty (I avoided Trauma as I like the souls idea too much).

Nowadays I got a new fairly large monitor and so I wanted to play again, but I am afraid the puzzle bosses would bore me again... After all if I understand correctly only Necrogiant, Alastor, and Cerberus are normal bosses.

To beat Alastor, you must also destroy statutes that recharge him with life, so this is not really non-puzzle boss and in the essence, the "puzzle boss" fights are not too much difficult to figure out how to kill them, if you want, look at this section of this site to figure out:

http://allaboutpainkiller.heliohost.org/bosses.html

That is fine, integrating the puzzle with the shooting is right. Instead (In my opinion) replacing the boss with a puzzle instead is not. More often than not puzzle bosses become a joke once you got what you need to do.

For example, the other shot-n-up Serious Sam also has some puzzle elements in the bosses (like frying Ugh Zan), but they were blended with the gameplay.
Ugh Zan won't become a pushover just because you understood the puzzle.

Wait until you come to Lucifer. I've found all the puzzle bosses before but in Lucifer it take me hours and hours and hours to find nothing. It just stand there and continue to fight. After a day or two i looked to a walkthrough. It was a bullshit puzzle.

True, that one was bad, though the map itself was brilliant. Anyway, a friend of mine thought all you had to do was shoot him while morphed since that's how he end up winning. He didn't notice he solved "the puzzle" while doing it.