I am a tinkerer. I always fiddle with rules endlessly. Bearing that in mind, some of what I suggest might be considered heresy, so take it with a pinch of salt.
1. TN4+ instead of 5+. Buying hits will be replaced with "take half". Suddenly, dice pools don't need to be so large and you don't need to scrounge for every modifier you can get. You can also afford to broaden your skills at chargen.
2. A firm dice pool cap of 20 dice (with an optional rule to break the cap for those who want it). Situational mods cap out at +/-5, and mostly are in the range of +/-3. Only give one high-level mod rather than lots of itty bitty fiddly ones. Combined augmentations (magical, cybernetic, pharmaceutical, etc) still cap out at +4, which stacks with the situational mods limit.
3. Standard thresholds should be 1-5 and no higher. Thresholds started at 1/2/3/4 in SR4, becoming 1/2/3/5 in SR4A, and then by SR5, the upper end was "8+". It's no wonder dice pools spiral so quickly in this game.
4. Staged Karma costs. Buying attribute ratings 2-4 would cost 10 Karma or one attribute point each. Buying them at 5-6 would cost 20 Karma/two attribute points each. At 7-9, it's 30 Karma/three attribute points. This makes creation/advancement so much easier to balance! Alternatively, use flat Karma costs (based on SR4A Build Point costs) with a single bump up to max out an attribute or skill.
5. Reduce the attributes to two physical, two mental, and two social, as follows: Strength, Agility, Cunning, Logic, Charisma, Willpower. Strength and Body would be combined into Strength, and Reaction and Intuition into Cunning. Make Athletics and Close Combat key off Strength. Use SR6 skills, or perhaps the Anarchy ones with a couple of tweaks.
6. Merge Magic and Resonance into Essence (and maybe Edge too). Essence comes in multiple flavours, and your rating (6) can be divided among them with certain caveats (e.g., you can't take both Magic and Resonance). The flavours might be: Magic or Resonance, Chrome, Edge. So you may have Magic 4 and Chrome 2, letting you take up to two points' worth of cyber, plus up to 8 spells or 4 Power Points. If you divide your Essence among multiple areas, you have less "capacity" for your main thing. Your Essence doesn't go down, it just gets shifted around, so you always have a maximum of six points between any of the flavours. If you gain more augmentations, your Chrome goes up and your Magic or Resonance may have to drop to accommodate this. Some points can't be shifted -- you need to remove 'ware to reduce Chrome (but you can use transhumanism to increase the amount of 'ware you can squeeze in per Chrome point). Initiation and submersion just add bonus dice and increase the number of spells and CFs you can learn, instead of raising your Magic or Resonance limit (but they might permit you to rearrange some Essence points if it makes sense).
7. Following on from that: cyborgs get transhumanism like in the 6e Companion. I'm calling it Metanoia, because it has multiple meanings that are apt here:
https://en.wikipedia.org/wiki/Metanoia The equivalent to metamagics would be adaptations. Cybersams deserve nice things too!
8. I think I'd make chargen simpler. Everyone gets the equivalent of around Priority D in all areas of their character as a baseline. You then get either one major advantage (roughly equivalent to an A or 200 karma) and one minor advantage (equivalent to a B or 100 karma), or three minor advantages. You can take no more than one minor disadvantage (equivalent to dropping something to an E) to take an extra minor advantage or to swap one of your minors for a major.
A major advantage would be a premium cyberdeck with programs, Magic or Resonance with free spells/CFs/etc, or a suite of top grade augmentations with relevant mods. A minor advantage might be a pair of cyberarms with razors, a bunch of extra points in attributes and/or skills, or a DIY deck/modded commlink with some minimal hacking abilities but no flexibility. A face could be made with three minors (+x attributes, +y skills, +z contacts) or a major and a minor (adept + minor social = social adept or major money + minor social = socialite face, etc). Optional rules would allow you to go totally freeform or to customise your choices further.
9. No more tracking ammo and the like in play. This would all be a factor of lifestyle costs and consumables rolls. Ammo might run out on a critical glitch but otherwise, don't worry about it during a run. At downtime, have people make a consumables roll, with any 1s meaning they incur extra costs due to unexpected repairs/delays/shortages/etc (maybe +5 or 10% of your monthly lifestyle cost per 1 rolled). Used gear ups the number of dice rolled, as would living beyond your means (e.g., living on the street but toting around SOTA gadgets). Free League has supply rolls which are a good model for this.
10. I might even use an abstract resources system altogether.
11. Put the Missions downtime actions economy into the core rules, and streamline it a bit. Allow enchanters and DIY deckers/riggers to make cool stuff for their next run. Working for the Man/Working for the People should be standard.
12. By default, gear should come in PACKs with each PACK itemised to allow customisation. People can then disassemble a PACK and swap bits out for other bits, if they really want to, but everyone can use something "off the rack". When someone buys an item, it should come with all the essential bits needed to make it functional, rather than requiring players to take an advanced course in fictional future tech and its interactions so they can actually use their commlink as intended.
13. No more aspected mages, per se. An aspected mage is any magician who hasn't mastered multiple aspects of magic. Players who want to play one can just buy Incompetent in two of their magical skills, can take a geas limiting their practice, or can just not invest in those skills. This makes trying to balance aspected mages much easier to do. I'd probably also keep mages as a A and B priority, with no other options available.
14. Mystic adepts are adepts who purchase each of the magical skills with Power Points. Mages might be able to gain a power point as a form of metamagic, but I'm undecided. I'm considering limiting this option to initiates in either case, which effectively bars mystic adepts out the gate, but I think giving GMs the option to allow initiation at chargen makes starting mysads much rarer, as in the fluff, without entirely removing them.
15. You can build your own decks from the start. Have this in the core rules. A DIY deck might just be a few commlinks spliced together with some other junk, or a cannibalised terminal with illegal software, but it is possible. You can't swap the array on DIY decks, but they're a suitable interim option for starting deckers. In time, you might even build something incredible.
None of this is playtested, and it's mostly off the top of my head, so caveat emptor!