What's the last carrier you saw in real life that had a battleship turret on it? Probably the only ships that follow this design philosophy are in the Soviet/Russian navy; they have a number of designs that integrate a short flight deck with a bunch of missile launchers or heavy gun turrets. However, these ships don't have the capabilities of full-sized carriers (not that anyone but the U.S. Navy have "real" carriers these days anyway).
That said, the Midway isn't really defenseless. As previously mentioned, it has ion cannons (my guess are fixed forward-facing mounts, these would be easy enough to hide embedded within the hull), and some really dense point defense. However, I believe that the Midway-type carriers are described as being able to replace a small fleet, not that they were 1-for-1 equivalent.
The chief motive behind the Midway (besides cutting down on EA/Origin's capship modeling budget) was as a cost-cutting measure. A single do-it-all megacarrier, with its point defense, fighters, Marine division, and science group, could replace the functions of a whole fleet of more specialized ships (science ships, Marine transports, escorts, other carriers). Obviously, the Midway, as a jack-of-all-trades, can't do things as well as more specialized designs, so in more dangerous times it makes sense to team up with dedicated capital combatants, like the Plunketts and Murphys, with the Midway taking up the carrier role.
All this theory aside, it makes it awfully convenient for the story writers to pull out all sorts of tricks without having to worry about how they're going to bring these folks along. (Marine assaults? Let's throw them in a hold somewhere. Independent operations far from supply? Let's have a hydroponics bay that can supply a whole colony. Strange alien threat? Let's hand it over to our science division. Hundreds of fighters and bombers? Let's scale the thing up to a megacarrier.) Personally, reading about the Midways in the Prophecy manual, I had the expectation that they'd all be destroyed early on into the next war.
