Air units. These things exist for the sole purpose of being annoying. You have to build special towers for them (which takes up room). These towers are useless against anything else. And they're very expensive. And worst of all, air units must be stopped quickly, because you can't recover cores from them. Overall, they don't serve a good gameplay function. I stopped playing the DLC missions because of them. They're not interesting gameplay; they're just terribly, terribly annoying.
Adding to that is the fact that missile towers overlap terribly. Highly upgraded missile towers can easily waste tons of fire shooting at already dead enemies. So you have to stagger your placement of towers. And remember: if an air unit touches a core, you can't get it back. So the only room you have is the distance between where the air units start and where your cores are.
Technically, you don't have to build Missile towers just to defend against the air units; groups of Cannon towers can do the job as well, and can also fire on ground units at the same time (Guns, while also capable of damaging air units, don't get much time to inflict damage on passing air units). Though, the trick there is making sure those cannons are in a good spot to fire on both air and ground units ... Still, you can go for a while without using Missile towers at all, depending on how you approach the map. Even then, you could probably get away with just one Missile tower near the beginning of the air units' flight path to soften the wave up for your cannons.
To pass a level? Yeah, prolly. To pass a level without losing any cores? ...unlikely. To pass a level with a good score? Not a shot in hell :p Missile turrets are just WAY too cost effective. Honestly though, this is a problem with like... every tower defense. Dt D averts it (Although mostly just by making AA Turrets unnecessary period) but the big problem is that turrets which are "only" AA have to be REALLY, REALLY strong to make up for the fact that they're just not useful the majority of the time, cuz otherwise nobody would ever take them over the generic hit everything turret. But then... you have to balance Air units to the uber-turrets. So everything else is basically useless/ absurdly inefficient vs them. That, or you balance it to generic, and Air units get roflstomped by AA turrets (for an example of both extremes, see, respectively... this game >.> and various WC 3 mauls) and TRYING to balance that feeling well is something that I've honestly yet to see ANY TD do particularly well imo (Although if anyone does find one, then please feel free to list it here :) I'd be interested).
Actually, it's quite easy to get away with only using a single Missile tower in most stages, if your positioning is good. In the right place, one missile tower can usually handle the first or second wave of flyers on its own, and thereafter a single upgrade is usually sufficient, assuming you have good placement of Cannon towers to supplement it. Multiple missile towers were only ever necessary in the final campaign stage, which was bloody hard all around anyway. Admittedly, flyers were very annoying, but their inclusion doesn't necessarily detract from the game, and adds a bit more complexity to the strategy which you have to account for.