TL;DR, the ship is gorgeous, but it is too simple. Adding more floors and reconsidering placement of systems would balance it out and make it a more rewarding ship to fly on.
I like the ship design, however, I think that system placement should be reconsidered. A sort of hierarchy of importance should exist, at least in my book. The hull is the most important, so engineers will always have to get to this place. However, it should be a risk when choosing to abandon that post for other places. By placing more systems in closer areas to each other, the risk/reward becomes more tempting.
For example, if the Hull was on a theoretical third deck by itself, it would be easy to sit up there and repair as required.
The second tier could include a gun, the main engine, the helm, and the balloon. This would make the engineer decide on whether or not he should jump down to repair that important system, and help the gun keep up its DPS, or let the Pilot smack the balloon every once and a while to keep it healthy. This would make climbing back up a mild inconvenience, but would still halt the engineer from abandoning the hull in crises.
The first tier, and lowest floor, could contain the turning engines and the remaining guns. This would make the bottom-most floor the most risky to fall to, because it would take a much longer time to get back up to the hull. However, the first tier contains the majority of the damage output for the ship because the engines control the ship's ability to keep a bead on a target(and the guns themselves, I suppose). The engineer would then have to decide if he should let the lower deck fend for themselves, or if a quick fall to help rebuild a gun could lead to a victory. This would definitely place more weight on the gunner's role down there, but the close proximity of all the systems would be balanced by the gunner's lack of tools, or requiring a gungineer to camp downstairs, and therfore, losing those two extra ammo types.
Because the Spire has its hull at the bottom, it is easy to reach by simply falling down the ladder carriage from the top-most floor. This allows a more risky engineer to float around the top deck. If the Jellyfish had a reverse of this, it would allow for the inverse event- spontaneous and quick-to-appear repairs all over the ship. Whether or not this is a good idea is up to debate.