Wow! That's a really cool, albeit unusual, starship design! I agree with you about enormous fanboy uberships, but I think that can be worked around. As long as it's not loaded with ridiculous amounts of phaser banks and torpedo tubes, you should be fine.
Actually, one way of explaining it's unusual design could be that it's not actually a Starfleet ship. What if it's an Earth civilian ship? Maybe some sort flying city. Civvies would live on it while it wanders around Federation space, visiting exotic (but safe) planets. Sort of like a massive luxury liner but with more permanent residents. That seems like the kind of thing a rich utopian society might build just because they can.
Actually, one way of explaining it's unusual design could be that it's not actually a Starfleet ship. What if it's an Earth civilian ship? Maybe some sort flying city. Civvies would live on it while it wanders around Federation space, visiting exotic (but safe) planets. Sort of like a massive luxury liner but with more permanent residents. That seems like the kind of thing a rich utopian society might build just because they can.