The problem, in short:
Air combat doesn't present interesting choices for a player in either its execution, when you are playing the interception out, or strategy, when you are thinking about where to locate your interceptors or how to arm them, and it doesn't feel good when you make those choices.
The problem, in long:
You can play the air combat fairly suboptimally by just equipping your interceptors, whether they're angels or phantoms, with two cannons each, and just fly at every existing alien craft and blow them up. You'll do some barrel rolling to dodge enemy shots, and you're going to take a few hits, but this strategy has worked enough for me to go all the way to day 200 against every craft that exists in this version of the game.
You can do a bit better if you'd like to, by equipping your phantoms intelligently with shit like torpedoes (a phantom with two alienium torpedoes and a Gauss Blaster will do better against an abductor than one with just two Gauss Blasters, but I'm not sure laser lances have a role at all), but you don't have to, and it doesn't feel terribly like you've fucked up if you didn't, nor does it feel terribly triumphant if you did, because, after all, no matter what method you've chosen to use, unless you did something really obviously dumb like fail to bring enough weaponry to actually down the UFO or just not fill your hardpoint slots and weight slots, then things will be kinda alright.
And it doesn't feel terribly triumphant if you have the ideal build to defeat a UFO because none of the options you have are super different. They all exist for the same purpose of downing UFOs, it's just that some are better at it in a situation and some are worse. I feel like I solved (an incredibly simple) puzzle when I put together a build that works against a UFO, not that I chose a strategy and then implemented that strategy.
Solutions:
The biggest thing to be done about air combat is to sit and think about what strategies should be possible in the game, and then consider what options players should be presented with to enact those strategies. Using guns and using missiles are not strategies because they do not imply different mindsets - they do the same things in different ways. Instead, these are some changes that might give room for players to create strategies to pursue:
- Some air weapons are decent while others are excellent, but costly to fire. Recast torpedoes as powerful, premium weapons where you have to manufacture each torpedo at the cost of cash and, for the more advanced types, alienium. Also give these torpedoes a chance to just explode some some UFOs' power sources when they hit, making UFOs give less alienium as loot. The point of this change is simple, to create a difference between interceptor loadouts that you use to down ships for cash and resources, and interceptor loadouts that you use for defending your bases and funding regions. Of course, you would then increase the difficulty of UFOs to make it so that it is difficult to defend adequately with ships that merely down UFOs.
- It is very necessary to invest in gadgets for your interceptors that take up weight in order for interceptors to accomplish some of the normal stuff they have been accomplishing without prior. Imagine if fuel tanks gave you like a full 100% extension to your interceptor's range, but without it you really could barely leave the range of your base's first radar array. You would make a decision about how much fuel to take or how much weaponry, based on how many bases you have and how necessary you feel it is to send jets around the world to prevent rising panic or let bases defend each other. Other gadgets that you might be able to kit out an interceptor with might be stuff like sensors to allow the interceptor to scan around it and see UFOs outside without the help of bases' radar arrays, or go faster on the world map.
- Make a lot of different levers for the options to kit out your interceptors so making your interceptors powerful in different ways have different strategic costs. Let's say we nix the system with weight, hardpoints, and equipment slots, and just say that interceptors have a missile, a cannon, and an armor. Then, maybe it costs an out-of-the-way research to improve your cannons, it costs way more money upgrade your missiles, and it costs way more materials to upgrade your armor. You balance UFO encounters so it will be generally okay if you have two of the three ship "parts" upgraded and updated, but you might have a bad time if only one of them is, and then you leave it up to the players which ship part they dump resources into upgrading.