It is good to get away from the standard Enterprise layout, good as it is (there's a reason they went with it originally after all). You can have downwards pylons work, a good example would be the Akira, D7, or Miranda. You can use certain tricks to make the design look less grounded. An example would be on the D7, the nacelles aren't vertical, they are angled inwards slightly, this gives a little "nervous energy" to the design, like someone on tip-toes. I think some refinement of the nacelles and pylons would help the design look a little less grounded.