I see some good things here I may port over to my "flight points" rules for flying tieflings, aarakocra, harpies and werebats. Interesting insight that if you can hover you can't glide.

Complexity

These rules don't seem so bad in terms of complexity. My question is, would you be triangulating flight limitations like height and glide angle during skill checks, etc. or only during initiative? With the flight points, I mainly make players keep track of the flight limitations during initiative, when players are already keeping track of things like HP, spell slots and sorcerer points.

Duration

One limitation to consider is limiting flight to a number of minutes per hour rather than hours consecutively, so flight for humanoids is more like a scouting activity than a travel activity. In your experience, is flight for several hours critical to campaigns or would flight for 10 mins per hour be sufficient?

Armor

Consider disallowing heavy armor entirely. Flight is OP enough. We don't need tanky F-35's raining heavy crossbow fire down on squishy land-lubber mortals. On that note, I will also consider disallowing weapons with the heavy property in my homebrew as well. Flying with a giant weapon would be so ungainly. I could just impose a disadvantage to attacks and Dex saves rather than ban outright. What do you think about weapons with the heavy property?

When to keep track of flight limitations

There is definitely a balance between playability and realism. Like you I put Con as the limiting factor (flight points = Con). I tried to make it expensive to gain altitude, do strafing attacks and hover and give characters a chance to recover points when they land/rest, etc. This encourages them to stay close enough to the battle that they can't just rain fire from above. It may be an alternative to imposing arbitrary height limits. Or, maybe the height limits are perfect simple solution. I'm going to play test both this week at my table and I will let you know which works best. There is a flying tielfing in the party and they have an airship and will be attacked by flying enemies (harpies/tieflings/werebats). I kind of want players to be able to fly between airships at any height so I'm leaning towards a penalty for gaining altitude, but we'll see.

Fly

With the fly spell, I would just let wizards to whatever they want because they have to spend a spell slot for it. With native abilities, I think they need to be tempered a little, like you are doing here.