100% first mod for most A90 years is the anti-wind buffeting kit. No joke.
Then I'd go wheels, exhaust, springs in any order.
Intake is more for sound and looks - I got the arma speed for the carbon fiber look (Under the hood most of my covers are carbon fiber for the oohs and aahs) and the sound. It sounds like the car has a blow off valve with certain intakes. It adds a little to the sound. I love it.
There isn't a lot to do outside of big upgrades like turbos, correct me if I'm wrong, anyone. And really, the car doesn't need much for the average person, it's pretty decent outta the box.
edit: Forgot the JB4 (Piggyback tuner) - many of us use it without issue if you want to lazy man or poor man's tune, but I believe tuning may finally be getting easier and cheaper (I'd look into that or someone will chime in, I'm sure).
Wind buffeting kit for sure. Will make the experience with the windows down better. Just make sure you get some 3M Automotive tape to apply it with; my first set from Armaspeed had some no-name tape, and one of them flew off on the interstate not long after install.
Wheel spacers is my 2nd choice without a doubt. 13MM front 15MM rear vastly improves the look of the car if you're looking to stick with the stock wheels for a long time. Inexpensive and very easy to install yourself. I recommend the Burger kit as I've used it for over a year without any problems: https://burgertuning.com/products/toyota-supra-wheel-spacers
If you like turbo noises - definitely an intake. It does not give you any additional power even when tuned, but you will significantly increase the amount of turbo noise you hear. I run the MST V2 intake and love the turbo noises so much. Another option is to get an intake resonator delete to achieve mostly the same effect while keeping the stock intake and spending much less money.
For exhaust, catless downpipe (if AZ doesn't test for smog, can't remember if they do) will make the exhaust much louder and give you good power gains when you get tuned. Catted downpipes still give you some extra volume and tuned power though. I run the FI Exhaust catless downpipe, it has thrown a CEL a few times when I'm too happy with the throttle before the car is warmed up, but usually it doesn't throw one. Exhaust is entirely up to personal preference, although if you have cash to burn I really like the Valvetronic valved exhaust because it's stock-quiet when closed and very loud when open.
As for tuning, if you just want a decent power bump JB4 is still pretty good, especially if you fork out the money for a Jesse tune like I did or spend the time on the JB4 log thread here to learn how to tune yourself, but the cost and turn around time to unlock it proper through FEMTO has been going down lately and JB4 isn't really that cost-effective of an alternative anymore.
So if you don't want JB4, it's a matter of doing a FEMTO unlock and then picking between MHD and BM3. If you want to go to a (reputable) shop for a tune, call and ask which they use/prefer before deciding, or if you just want to roll with the off the shelf maps, basically research which one sounds like it has the featureset and future potential that you prefer. (Note: A small % of 2021's are already unlocked, specifically if they were built before 06/2020. You can check the manufacture date in the driver's door where you would find weight and tire pressure info. You can also get an OBD link and use the MHD app for free to check if you're unlocked or not.)
An XHP transmission tune is also nice to do. Will make your shifts quicker/snappier, especially in manual mode, and will let you customize how the transmission behaves, such as always starting in 2nd gear, and setting your own shift points for both normal and sport modes.
There is also bimmerlink/bimmercode, which is worth it if you want to code in some extra/missing functions from the platform's BMW counterparts. You'll have to read online about everything you can do on the Supra with those apps before deciding if it's worth it to you.
Lowering springs are a decent mod for basically any sports car, you just have to determine if it's worth scraping more.
I'm a big fan of adding a small spoiler on the trunk, it just adds a lot to the look of the car to me. They tend to be inexpensive, and most of them you can install with only 3M tape (I used 3M tape on mine, albeit a lot of it, and over a year later it's still rock solid)
A front lip of some sort is also a nice visual upgrade imo; I feel that from some angles the stop lip is just too high up, adding a lip greatly improves this, at the cost of more scraping when inclines meet flat roads. I ended up getting a replacement lip that's a black plastic ripoff of the Adro lip on Amazon for cheap and it's surprisingly good fitment.
Side reflector mods are also nice, either delete-inserts entirely or black tint overlays. Relatively cheap and easy, and the side markers look like afterthoughts anyways. It's debatable whether or not this hampers safety at all; I personally feel like if you're not doing a a "murdered out black" build there's not really anything to worry about.
Hopefully this wall of text helps in some way; please correct me if I'm wrong or just plain stupid on any of this.
TL;DR;
QOL: Wind buffeting kit, Bimmercode/link
Looks: Wheel spacers, front lip, spoiler, lowering springs, side marker delete/tint
Sounds: Intake/Resonator delete, downpipe, exhaust
Performance: Downpipe, Tune (JB4, or better yet MHD/BM3), XHP