JJ2 was much more violent than JJ1. In JJ1, enemies would just disappear when destroyed, and occasionally you'd see the tiny explosion made by a bullet hitting a wall. In JJ2, enemies splinter into a thousand pieces which fly in every direction before eventually decomposing on the ground.
In JJ1, when you died, you'd crumble to dust, leaving your gun, which still maintained the ability to jump around and shoot at things. In JJ2, you actually suffer major injuries and fall to the ground dead, or explode with practically no remains in the case of Spaz. Especially in the early versions of JJ2, where the bodies wouldn't go away after you kill them, but just sat around being dead all the time.
And there is no possible way JJ1 could have better graphics. Everything in JJ2 is drawn well over a long period of time. JJ1 was essentially slapped together, and despite having the same graphical power for creating tilesets, came out with far inferior graphics.
...and he has blue goggles. Like Bucky'o'Hare.