Nova Bomb is somewhat unique in that every upgrade changes the method of delivery. I wouldn't say any one is definitely better than the rest. Which one to use depends on the situation and more so on your playstyle. What [b][u]Shatter[/u][/b] does is elongate the AoE. Counter-intuitively the AoE is not actually larger most of the time, it just changes shape. It also is theoretically the weakest in terms of damage. The wider AoE makes it easier to hit targets because it creates a larger margin for error. The further the three projectiles travel the further they move from each other. This can increase the size of your blast radius even more, but if the projectiles get too far apart they will not have overlapping blasts. This creates a very large but comparatively weaker explosion than when they are closer together. Given that each projectile is created in succession from left to right rather than all simultaneously it is actually possible to control the size of your spread. Turning the camera left while using Nova Bomb will make a tighter spread while turning the camera right while using Nova Bomb creates an even wider spread than normal. [b][u]Vortex[/u][/b] is the most basic of the upgrades (and is probably why it's the first one you unlock). You simply throw one large Nova Bomb that always does consistent damage. The vortex it leaves does two things. First it continues do damage to anything that survives the Nova Bomb, which is why is has higher potential damage. They other thing it does is provide area denial. While the Vortex exists nothing can cross its path under threat of being killed by it. It's best against that are large and slow, like bosses, as it will take them longer to escape the vortex and thus take more damage. If you're smart in how you use it you can actually trap enemies inside the vortex where they'll take even more damage. Vortex often takes more thought to make use of its potential, but can be very useful in the right hands. [b][u]Lance[/u][/b] is in my opinion the most drastic change to Nova Bomb. Lance can make Nova Bomb much easier to use by increasing its degree of precision, as opposed to Shatter which reduces the need for accuracy. The complete removal of the arc makes it much more effective at range. Where you were aiming when it fired is where it'll hit. There's no trying to quickly estimate the trajectory. The additional increase in speed means that it'll be that much harder to avoid. The flat damage increase they added to it also makes it appealing as it does more damage than Shatter and the damage is more constant than Vortex. Overall i'd say that the appeal of Lance is reliability.

Shatter is anti-bubble goodness!

I like Shatter for groups of enemies or ones that might dodge. Combine it with Bloom perk and you can wipe out large groups as they all explode together. Lance or Vortex works good on isolated slower moving targets.