For everything outside of the levels, Balloon Invasion uses the same engine as GemCraft Chapter One. So, you still have a side-scrolling map, levels you have to unlock, skills to upgrade, etc., except that it's all themed for an artillery defense against an invasion of hot-air balloons and zeppelins dropping bombs.
The levels are what make this a completely different game. You are presented a side view, with your main flak gun at the lower right of the screen. Balloons of different shapes, sizes, and speeds come floating from the left to the right. You need to aim your flak gun at the balloons, leading them the appropriate amount. And exactly where you aim is important, as the flak shells need to explode at a certain point in space (so they're not like bullets or lasers, where anywhere along the trajectory is equally good). The key difference here is that you are constantly actively firing, making this game feel much more real-time than GemCraft, where you place towers and gems and then just sit back and let them shoot automatically.
To keep up the excitement and to help you out, you can also place other guns (which come in different types and which fire automatically) and call air strikes. Your other guns usually get destroyed throughout the battle, but you only lose if your main gun gets destroyed. This is the other main difference between Balloon Invasion and GemCraft (and most tower-defense games): it doesn't hurt you if the balloons make it to the other side of the screen. Yes, it hurts you if they drop a bomb on your main gun, but not all of them do (if you have other guns out, they will often drop bombs on the other guns first, and balloons have a limited number of bombs). The balloons somehow magically appear on the left again after going off the screen on the right, but I can forgive this minor unrealistic aspect.
So while Balloon Invasion probably won't keep me playing as long as GemCraft Chapter Zero did, its different gameplay mechanic makes it novel and will keep it interesting for a little while at least.