I mostly ignored the Gummi Ship minigame during my first pass through Kingdom Hearts II. I only played through the stages to the extent that I had to in order to open up the paths to new worlds. While I attempted the higher level modes a couple of times to see what they were like, I never seriously challenged them. In hindsight, I never even opened up the Gummi Editor once during that play-through. Yet, I have ended up spending hours playing the minigame so far on my current run. I have discovered that it can be a lot of fun, and I have designed several ships of my own with the Gummi editor. What really makes the Gummi Ship minigame of Kingdom Hearts II really outstanding is how it supports both ways of approaching it: rewarding those who are interested and staying out of the way of those who don't care for it.
All told, the Gummi Ship minigame is extensive enough to practically be a full-length game in its own right. There are almost as many Gummi Ship stages as there are worlds in the main game. While each stage is pretty short and quick, every one has three levels of challenge, each with different enemy patterns, goals, and treasures. Since the player has to both earn a high rank and defeat certain rare enemies on every difficulty level in order to get all of the stage's rewards, there is a lot of replay value to be had in scouring a level for treasures one missed on the first pass. On top of that, I have had a lot of fun playing through old stages with new Gummi Ships to see if I could get better results with new combinations of parts. So far, I have built a cannon-focused ship, a laser-oriented ship, and a ship loaded down with Meteor-type weapons, and I still need to try out slashing weapons. There is still a lot more for me to do with the system.
As extensive as the Gummi Ship system is, the game doesn't require the player to mess around with it at all in order to clear the game's main story. While the player needs to fly through each stage at least once in order to open up the routes to new worlds, doing so is not a very hard task. Unlike the higher level modes, where the player has to eliminate hordes of enemies quickly and efficiently in order to get a high score, opening a route only requires the player to survive the stage. In addition, the game doesn't require the player to design ships with the rather complicated Gummi Ship editor, if the player doesn't want to. For this reason, the player is given pre-built Gummi Ships as he progresses through the stages. While potentially not as powerful as custom-built models, these pre-fabricated Gummi ships are more than good enough to get the player through to the end of the main plot. I made it through the game using nothing but these pre-built ships on my first go-through.
Other than needing to open up the routes, the Gummi Ship minigame and the main game don't overlap at all. All of the parts needed to build Gummi ships are found as rewards in the Gummi Ship minigame. Building a powerful Gummi ship doesn't give the player any huge advantage during the main game. Both of these a good qualities. If the player could get an advantage in the main game from the Gummi Ship system, it would force people who were otherwise uninterested in the minigame to play it in order to get that benefit, which can frustrate players quickly. If Gummi blocks were regularly found as rewards in the main game, players who didn't enjoy the Gummi Ship minigame would get annoyed that they were finding useless treasures. With no overlap, players who really enjoy one of the two games don't need to force themselves to sit through the other unnecessarily.
It is worth noting that many of these elements are significant improvements over the original Kingdom Hearts' Gummi Ship minigame. In the original, there were no prebuilt Gummi Ship models, the player had to fly through Gummi Ship stages regularly, and Gummi blocks were regularly found in treasure chests. The tighter integration of the Gummi Ship minigame more closely to the main game as seen in Kingdom Hearts 1 did nothing to make me like the system any better, and did lead to many of the problems I outlined above. A good minigame should be deep and rewarding, but otherwise unobtrusive.