Speaking of waves...
Personally, I was hoping defense would be more wave based, similar to tower defense games and TF2's Mann vs Machine. Various pre-set compositions of enemies are spawned in each wave (early waves are often single types of enemies, later waves throw in more combinations). This would've given a bit more tactical depth than just shooting everything that moves and hoping a carronade ship isn't on your rear if you're not in the Stormbreaker.
For example: first wave spawns nothing but the short fire ships. The second spawns short and long kill ships. Third spawns short and long disable ships. Fourth spawns every type of short ship. Fifth spawns every type of long ship. Sixth sends a mix of short and long ships of all types. Seventh is the boss and his support. Some waves have critical weaknesses that can be exploited, and make players feel smart for exploiting them. Other waves are well-rounded offenses that demand the best of players, making them feel proud for their proficiency. Right now I feel like I'm running errands and hoping that the win-the-game ship doesn't burn engines straight to the base.
On other gripes with defense:
They want to tell a story where giant spider-drills are sabotaging this geothermal station, and the enemy forces are trying to protect the drills and contribute to the sabotage themselves. However, the drills can be ignored indefinitely in practice, there is no urgency to destroying the drills other than risk of your crew abandoning out of boredom. They don't do any damage to your structure, the boss doesn't seem to spawn until all or at least most of the drills are destroyed.
There's also a problem with 1 ship defense. The devs are trying to balance 1 ship defense, 2 ship defense, 3 ship defense, and 4 ship defense all at the same time. 1 ship defense means that a single ship has to go out and destroy all those drills themselves while simultaneously fending off ships from attacking the main base. All other numbers allows you to have a dedicated defender and a dedicated assault ship, splitting the task up. I feel like they are trying to make the same mission be doable regardless of number of ships, but I do not think the devs should worry so much about 1 ship defense. If anything, make it the most difficult and demanding so players are encouraged to work with multiple ships. All missions should be easier to handle with more people as opposed to less. You have twice as many guns with 2 ships than 1. And twice as many ships.
I would personally like to see the drills made into threats spawned with or in between waves as a way to force defenders to react, rather than being the primary objective of the mission. Make it so that drills do damage to the base over time if left unchecked, forcing someone to react quickly to deal with it. This allows you to do stuff like spawning 4 drills with no support ships, and still having a high-pressure situation where speed is important, lest you lose to the drills. For any MvM players, think robot tanks. The ones that often spawn in addition to the ground troops and, while having no offensive capabilities, are very tough to kill and will single-handedly cause you to lose the game if they get to their objective.
I keep bringing up things like MvM and Warframe in regards to the Alliance content because they are two rather successful competitors. Sometimes I really wonder what kind of research Muse does when designing these modes. Do they look at what competing PvE games do and try to iterate and innovate off of those, or are they trying to come up with something completely on their own? There is nothing wrong with standing on the shoulders of giants.
As a side note, they dismissed Warframe as being a "2-D" game in dev chat before, talking about how it wouldn't work quite the same. Except that's not quite right. The alliance maps don't make enough use of height to be any more than "2-and-a-half-D", as movement is primarily 2D and height is mostly used to make sure you don't run into low-lying obstacles and can point your guns at the enemy. There's no real stealth element since ships instantly spot you, so it isn't like flying above the clouds or keeping low to the ground helps much. Don't dismiss what they have done with their various modes. There's a reason they are so successful that they are still putting out regular content updates and upgrading the game.
Also, Warframe is more 3-D than you think, if you actually use the movement options. I've had a lot of fun in some missions where I am jumping around on equipment near the ceiling to avoid detection from below, and there are a lot of very vertical areas in various maps where you can escape by falling down or parkour'ing your way up.
I just really want Alliance to be as successful as possible so they can get back to adding content to Skirmish.