My nomination is the Maestrom skin for the Fleet Escort. It looks like a turtle that has mated with a facehugger. Yet it also looks cool too in a flying tank kind of way. Whats your ugly ship of Sto?
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By far the Olympic class and variants. The single ugliest has to be a mix of the 3, but frankly, even trying to take the least ugly parts of all, you still end up with a monstrosity, begging for the sweet release of death.
Most Ships get uglier when damaged, the Olympic improves, the "ball of fire" look suiting it best.
Second place is between the Kar'Fi and the DSSV variants.
On the other hand, I don't get the hatred oft-directed at the Hermes (and variants): that Ship exudes menace. It's not chelonian, it's lupine!
Though it might be too menacing to fit into the whole Starfleet ethos.