Well, I'll be honest, when KH first came out, I was HYPED for the Gummi Ship. I love building models and stuff, and this seemed like awesome Lego + shooter. The reality was something else though, and it was boring, pointless and just wasn't very fun. The parts weren't great, the stages didn't really have any flair to them, and it was a really boring and shitty shooter minigame with average customization of the main ship.
Then KH2 was coming out and they promised a total revamp of the idea. It sounded awesome. Panzer Dragoon style rail shooting! More weapons and customization on the ship! Well.... it was certainly better, but it still wasn't very good. Kinda average and fun for fans of rail shooters (I enjoyed the levels, but didn't really want to replay them), but way too button mashy and the customization was still kinda ugh.
Now with BbS, he drops the Gummi Ship entirely (duh, hasn't been invented yet!), and you just move between the worlds the same way as you do in KH2, on a map, except without the lame minigame stages inbetween. Instead the major "minigame" companion this time is the Command Board, and HOLY SHIT IT'S AWESOME. So yeah, I think Nomura has definitely been trying to improve on the KH formula with each game, and it's very visible in all the little upgrades, changes, and design decision each subsequent game has.