Apologies for the long response here - but you asked for feedback, so here's some of mine:
For those wanting a summary: in short, my biggest problems with war levels are that they make it virtually impossible to move around/maneuver to different parts of any world more than once or twice ever and they remove much of the incentive of having a military at all, promoting instead isolated, single-player play on worlds besides FB.
You can only really take c3s once in a cost-effective way (up to as you said, to maybe war level 6), and then you're kinda done FOREVER with your account from being able to move around easily. Example: The core of my empire is over 10,000km from Gaz. Optimal fighting range is under 3500km (which is fighter range) if not closer. Heck, even land based cruise range is 5,000km. Being that Gaz is now War Level 11, he has to fight a war level 12 c3 first to even really get range on me. Shooting from that distance with conventional missiles doesn't make sense against any sort of federated air defense, and I'll touch on why navies aren't a good option in a second. Conversely, I'm war level 3. I can hop across taking a couple of c3s to move next to him MUCH more easily and cheaply than he can on me.
As such, moving up in war levels makes you less able to fight effectively against players (I will never do so unless necessary). In large, past wars, I'd take 10+ c3s (outside of fighting my actual enemy) just to be able to move into position to fight, to support allies, etc. Ally on the other side of the world under attack? Good luck to them now, because you're not coming to help. There are so few people to fight anyways, and now you're limited greatly by location. This is why I think having time-limited ability to fight at war level 3 could be helpful. IE, even if you're above WL3, you can fight one war level 3 c3 per week or something similar to Gaz's proposal about opting to stay WL3. ANY improvements to being able to maneuver would be helpful. Otherwise, you're stuck with whatever limited range your countries have forever unless you want to spend 30 gold coins (a month's registration worth of gcs) to buy a new c3. That's too steep of a cost to be worth it.
Yes wings do help - and probably are the best defense, but they're expensive (like all weapons groups). Most players don't have wings up - largely because they can't or don't want to afford them + ammo upkeep costs, and also because there is no incentive (why not just stay in war level protection for free?). If you're new and have a 25-30 million pop country, you likely can't afford to keep more than 5 or 10 wings up. That'd take up all of your profits in maintenance, and acquiring that much ammo and weapons is challenging as it is when you make so little profit (relatively speaking compared to those costs). It COULD be worthwhile if you could cost-effectively expand into and keep a number of war level 1-3 countries to increase your total income but instead, you're forced to fight increasingly more difficult AI defenses and to lose FREE, PERMANENT protection.
I honestly don't think you're given enough high quality weapons to have success against a c3 when you start anyways - especially if you're a new player. Don't believe me? Try it yourself. The weapons quality you have is too low and you get mauled by c3 air defenses. Matthew of Batavia recently made a forum post about this, which I completely agree with. He's not a new or an uncommitted player, and he had difficulty. As such, it's fair to say pretty much every newer war player will have difficulty fighting starting level c3s at all. The number of brand new players I see on FB who create a country, declare war, fail, and then quit the game is very high. If they'd have won their first fight, things might be very different for them. Better weapons and basic instructions for how to fight would be helpful here.
If, instead there's an option to be entirely safe forever and stay in war level protection, it's the OBVIOUS choice for most players. There's no benefit to being at war level 3 and being vulnerable to attack when you could just stay at war level 2 or lower. A few gold coins aren't worth it when instead you could have a billion population empire printing money forever with zero military costs. As of a couple days ago, there were a total of SEVEN players on White Giant (the most player-populated world) who'd made it to war level 3. Everything I'm saying could be totally wrong, but you can't say that players are progressing through war levels regularly. They either can't or are choosing not to. I have ideas here, but this is already too long of a post
Regarding your comment about how strong navies are: Only the very richest of players can afford substantial navies, and navies can be neutralized too easily. Honestly asking - how many players have substantial navies active right now? Is the number more than 2 or 3 per world? I doubt it. Additionally, I disagree that they are strong enough to be able to take on air defenses in a cost-effective manner - especially if there is a federation air defense. As you yourself said, air defenses can cause substantial damage - and doing so to an attacking navy is EXTREMELY costly for the attacker. If you have allied air wings responding from your federation (1500 interceptor response), it's virtually impossible to push through with a navy. This said, it just means your effective attacking range is limited. You can either buy an extremely costly navy and take terrible weapon trades against interceptors... or just stick to your little section of the world, and not interact with anyone outside of that.
Finally, I think one secured main per world is enough to keep plenty of assets safe, like it used to be. If not, why don't you try a "peace" world. We have a war world, why not have the inverse where players NEVER risk war and can play the single-player game. There are currently zero active wars on LU, so we're already almost there anyways. 8 TOTAL player countries have been taken on LU by current players since war levels started. 8. Ever. And I believe most were against inactive players by members of the same federation. This seemingly amounts to virtual extinction of the war game, - or explain to me how I'm wrong.
See how many players choose a peace only world, and if they do, great - there's a place they can play in peace. I think most players join the game thinking there is a chance of being involved in a war at some point, and then slowly learn that it's not worth it to go to war level 3. As it stands right now, I fear that most players aren't willing to risk complete elimination on the war world, and there's not enough incentive to come out of war level protection elsewhere. This generates far fewer player interactions, and has moved the game largely to single player mode (though it's advertised as a "Massive Multiplayer Online Game"). What's the actual benefit to you of joining a federation if you are war level 2? There isn't one.