...plus the Delta Flyer is still something that is chargeable via the C-Store, the Captain's Yacht? Totally Free. (Assuming you pay for 400 days of gameplay...)
Free things shouldn't be quite as good as things to pay for, otherwise their model of generating extra cash via the C-Store would be broken. Why buy something that's crap when you can get better for free?
I can't remember the stats but the Yacht is only very marginally weaker in things like turn rate, inertia and speed. The hull and setup are the same and only the ability is different but considering it's free and the flyer will be craftable soon I'd not worry either way.
I would say the Runabout, Captains Yacht, Delta Flyer, and Vulcan Support Craft are all comparable to each other. It just comes down to your preference and play style. At least that is my opinion.