Every single, every single set piece fight is unique in design and what you need to do. It's one of the most tightly designed and polished games I have ever had the pleasure of playing.
I gotta say... once I arrived in the Island, a bit of boredom because of mindlesssly shooting things began to set in. it was all cover/shoot.
I see your point, that every time you crossed a checkpoint, there was a "twist" to the shooting and killing but in the later part of the game it began to drag a bit.
My perfect RE4 would be half the Island with a short leading-up to the fight with saddler.