I was sarcastic there. Or I wasn't. Anyways.
The thing is, I understand where IA properties come from, but then we run into practical things:
You've been beating this why are IA moves better drum for like days, so it was a pretty safe assumption you have no idea how this actually works.
IATP hits faster possibly to make up for the fact that animation features character going to the bottom of the screen which means that if executed mid-jump it will be too slow. Okay. So we must alleviate the issue. Obvious solutions include speeding up the move depending on height; dropping that requirement to descend to very bottom, turning it into fixed range to travel before character disappears. There are many ways to make sure move won't suffer if used in the air unless it's not supposed to be good under those circumstances. By making it flat out faster you make sure it is to-go move considering that this game has no minimum height requirement to speak of.
This means that either you're doing this on purpose (creating execution tax) or you've screwed up opening the move for potential abuses to make it faster than intended (which is I'm fairly sure not the case - NRS sure know much better at this point). Or you're just lazy and don't care, but c'mon...
Again, this is not a new problem. Nor is it an MK specific problem. The only difference is most games do not have air moves that mimic their ground versions as closely as MK games do. So Akuma's fireball is never going to be more useful than his ground fireball. Most games don't even have any moves that act like tele upper or IAGB because most dev shops don't have the balls or desire to try and balance them. Capcom went balls out with Marvel 3, and it wound up with one of the sharpest most well defined tier lists in the universe, predominately because of which characters have an air game and which don't. But still, go watch a gamerbee match in sf, watch any half decent Filia in Skullgirls or chipp in guilty. Or better yet, go watch any classic MvC2 match. Any one at all. Literally every move in that game is done better if you use its instant air version. This has been a constant thing in fighters since the first SF2:HF player picked Ken and realized he could combo off tatsu if he did it low in the air instead of off the ground.
The reason it is generally tolerated from a balance perspective is that the benefit of instant air use is usually offset by the difficulty of performing it immediately off the ground. And more often than not, if you blow it, you're going to pay for it because now you're hanging in the air defenseless. Unfortunately, MK already has the lowest execution barrier of just about all fighting games so naturally, its instant air game is easier (and therefore more effective) than most.
Same goes for IA projectiles - if devs didn't want them to be hard but effective move relying on execution, they sure could make sure character suffers additional recovery once he lands, but they didn't because they want them to be more than air-to-air projectiles. But at least these aren't no-brainers as of late as IAFBs actually have drawback of not being true mids even if original projectile is (unless we have characters with hilariously large crouching hitbox), for example. Unfortunately, with likes of Sektor's IATP there's no real choice and no guessing game to be made out of it, you only need IATP. Heck, you can even input it like IATP if you're canceling string into grounded teleport and game will still read it as needed, same with actual air TPs. You end up with udb4 move you need for everything TP-related and db4 input you don't ever need. I don't think it's too far-fetched to ask why does "db4 grounded move" even exists and "udb4 move" isn't given bd4 input then.
Congratulations, you've just graduated from fighting game design academy with flying colors. Unfortunately, fighting game
making academy is not a magical funland where everything a designer wants to do is possible. If it was as easy as you say to just "make moves lag more depending on how high or low they are used" every fighting game would do it. In reality, almost no games do it. Just about every recent 2d fighter is chocked full of moves that are better (and in some cases only useful at all) with air or instant air timing. Even marvel, a game that is played at least 50% in the air, doesn't variable air lag on specials and it has hitstun decay and variable pushback. Why? Because since its pretty hard (or at least it was, before hitbox) to use instant air timing consistently, its okay if it introduces a slight increase in functionality. It's the same way that wave dashing, armor cancelling, chicken guarding, crouch tech, etc are all "rewards" for maximizing your execution, so are instant air type punishes and reads. Do you think Capcom planned out every 1f link in SF4? Sure, they maybe planned a couple, but overall I'm sure they were just like, hey, if the players figure it out, so be it.
As I've said, it's impossible to think that devs overlooked how people were practically using their tools for two games already, if they left something like that in the game, they sure did this on purpose.
Its a bigger overlook to assume that there is a harmful agenda at work here, and not simply an oversight or design impossibility. The same way that shoddy collision boxes or glitchy animations are just a thing you have to accept from time to time. The "left in on purpose when they could've easily fixed it" scenario you paint is absurd. SF4's links are better than chains and Tekken's JFs are deliberate gameplay systems used to encourage or reward good execution. MK has nothing of the sort. The last MK game that tried anything akin to it was MKvDC's promoves and everybody hated it, which is why we now have stock EX specials.
More to the point, the solution is not just as simple as making all moves the same speed in the air and on the ground. It might work for tele upper and tele stomp, but those pale in comparison to what it would do for gas blast, or fan throw or square wave, or any number of other moves that would be godlike on the ground with airborne timing, or worthless in the air with ground timing. The dream of height based variable recovery / trip guard is a beautiful one, but at the moment its just a pipe dream. Even then you add a bunch of lag to an air projectile, it might be unsafe on hit at certain heights. Would anybody really like a combo that you get punished for cause you hit it a little too high?
No. The only real way around it is height restriction, which, as you've conveniently ignored, is already in Injustice (and I assume MKX). Wether or not its implemented at current who the fuck knows but odds are they're waiting to address that along with all the other balance concerns once the cast is closer to finalized.
Still, even if they do restrict it all to hell, that's not going to stop players from trying to find the lowest possible execution point and find new ways to use air moves. That's the beauty of actually playing and exploring the game instead of just immediately chucking or ignoring a move because it appears "useless". Remember back when Tom Brady, a legitimate member of the community and the QA staff said that MB Trident Rush was "not a great move"?