The vertical will give you much greater stiffness and greater resistance against hysteresis (twisting). The x and y axis will be controlled by the table and with proper way covers can be protected from contamination.
The bridge type design can work well with sufficient stiffness if the upright castings are beefed up enough in their design. The weakness in this design May allow for hysteresis (twisting) during cutting conditions, but if the castings are heavy and sturdy enough..... This problem may be eliminated, or reduce to such a degree that it will be negligible (maybe only .0002-.0003" maximum).
Also, a Gantry design in many cases allows for a larger work envelope, and the greater flexibility of adding on a tombstone or indexing head..... Simply because there's more room to do so.