I see a few (or more ... I started out with two, but it just kept growing! ) downsides to NPC cap ships. TLDR below.
First and foremost, it lowers the number of scenarios you could have with cap ships. It limits the players ability to control their surroundings, which I believe is a bad thing. Even if there is a large number of 'paths' that a cap ship could make, it's basically like going into an ice cream shoppe and their only choices are chocolate and vanilla. Sure, they're great and all, but what happens the umpteenth time you eat chocolate ice cream? What about ginger peach ice cream? Denying players their ginger peach ice cream denies choice, and in a huge environment like Battlescape, there's going to be many instances in which players would want a cap ship to do something or go somewhere to make it worth while to cater to all the variable scenarios.
Second, it would make the development (and modding) harder. It might sound easier saying "yes, preset path ALL CAP SHIPS", but what about... procedural generation? If we get a new system every game (and I see no reason why not), my guess is (not being a programmer) there is going to have to be a hefty algorithm to draw paths every instance. I see endless threads of "Cap ship did this weird thing", "Cap ship here plz", etc. It's either that or have poor ol' Hutch hand draw all the paths. Having player controlled cap ships with decent flight controls eliminates this.
Thrid, it would halve the number of player flyable ships. This might be a good thing, allowing the devs to focus on honing the other 3, but there's extra pressure to make sure there's enough variety in gameplay and/or load outs. Given the scope of IB in terms of possible combat scenarios, I doubt this would be too big a problem.
Forth, the KS kindof did say that we could fly cap ships. As previously stated, not strictly legally binding, but it would be a disappointment for players that were expecting....
...Fifth, Homeworld-esque RTS. 'Nuff said, really.
Sixth, the corvette becomes the biggest flyable ship. It's nice and all, but it may turn people away if they aren't as interested being in a small fighter when they really want to sit back and tank stuff in a monstrous cap ship.
Seventh, it may subtly change the focus of the game. I'm not as sure on this point as on others, but only having access to the smaller ships would have the game focus more so on the combat and less on the strategy. After all, if the cap ships are fixed on paths, then there are only so many strategies and options available to be exploited. Another side effect, guessing the other team's next move becomes easier. It would tilt the balance more into the tactics corner and less of the strategy corner.
TLDR; Say no to paths.