Okay, I'm taking a step back and looking in broad at the things that bug me and making a list. It may not include everything, as I may have forgotten a few things, but it covers a lot regardless.
[ Spoiler ]
General System
-TN5 and most tests being opposed leaves very little granularity with most tests. Characters with small dice pools frequently find themselves extremely likely to fail even at the simplest of tasks.
-Using a different system for building and progressing characters forces metagaming on character creation for efficiency, this should be resolved.
-Karma Rewards are too subjective, leading to vastly different perceptions of what should be rewarded. Karma rewards should be more standardized.
Attributes:
-Attributes are far too important, potentially contributing far more to the dice pools of various tests than the skills or any other mods. Training should be necessary to be good at something.
-Attribute mods are too easy, with someone who starts with a 1 in a stat easily able to raise that attribute to 4-5, or even to cap with cyberlimbs. Unaugmented stat should matter more, playing into both max augmented stat, and also being the softcap for skills (as opposed to an arbitrary limit, or a hard cap)
-With attributes starting at 1 and needing to be bought up, dump statting is heavily encouraged, and racial penalties to attributes aren't felt unless they affect your specialization. Attributes should start at average for the race, with the ability to be bought down with negative qualities.
-Body and Willpower are largely useless stats, used only for resistance tests, and not tied to many skills. These could be made into derived stats and the only thing that would really need to be modified is racial bonuses.
Skills:
-There are many skills ungrouped that could theoretically be a part of groups with other skills. Having all key skills a part of a skill group makes it easier for a new player to pick up a skill group relevant to them and go without needing to know what each skill individually does right away.
-Basic skills for interaction with the world (Computer Use, Data Search, Charisma based skills) need to be bought just like everything else. New players will frequently be missing these skills, and even veteran players are often tempted to make a hyperspecialist who seems incapable of talking with people without making a fool of himself, or use the matrix for even basic functions. These skills should be available at a low level to players for free at character generation. They could be bought down with negative qualities.
-Skills capped at 6 leaves most characters feeling like they hit a glass ceiling even as early as character generation in key skills. Additionally there is too little difference between a high skill (legendary) character and a low skill (barely trained) character.
-Skill costs ramp up too quickly. They should ramp up slower at first, with a sharp spike based on the attribute the skill is linked to. So say you have 6 agility, you might be able to get to 9 skill at a fairly reasonable cost (by fairly reasonable I mean roughly what it costs to get to 6 skill now), but once you hit 10, the cost suddenly jumps up a significant amount (this can either be a scaling amount, like say 1-3 per rating over the limit you go, or a sudden sharp increase like a flat 10-20 higher, depending on how harsh you want the softcap to be)
-Combat skills are pretty overpriced, and are overspecialized. You have to buy a weapon skill for every weapon type, yet a mage only needs to buy one spellcasting skill, and can use all schools of magic equally well. A hacker can buy a single hacking skill for his hacking needs. Firearms should be reduced to a single skill, with a new skill group that includes Firearms, Gunnery, and Heavy Weapons. A similar consolidation could be done for melee weapons.
-Gymnastics should not replicate the effects of dodge for free as long as dodge remains an individual skill.
-Skill development time is a crapshoot. While sure, it's realistic to have to spend weeks or months training to increase a skill, fact of the matter is we are playing a game, and in a game your character taking 3 months off to spend his hard earned karma just doesn't fly. This and equipment gathering time are the two biggest annoyances in the game. They're there to attempt to simulate reality, but serve no real balance purpose.
Magic:
-Magic is too hard to resist without a mage present. There needs to be some way to add to the resist roll for spells without having a mage. Also consider Direct Spells having a base threshold requirement of target's Will.
-Direct Spells are way better than Indirect spells, providing similar or better effects for far less drain. This must be addressed.
-Adept Powers are way too expensive, they need to be reduced in cost. Something similar to The Ways (a quality that reduces the cost of a few powers chosen by you and gives a bonus to initiation grade) should be generalized and made available.
-Magic always beats not magic. Mundanes need some toys that magicians can't use effectively that are effective enough to make up for the fact that they don't have magic.
-Magic should be about introducing cool things. An adept should be doing crazy off the wall shit, not just getting +3 to a skill. Skill bonus powers should be eliminated (stat boost powers can remain, as the magic alternative to cyber/bio, but should be cheaper), but the main reason you go adept should be for things like elemental strike and distant strike. Things that add new options to what you do. Things like this should be introduced for the various adept roles, including Gunslinging (I have a homebrew for this already if anyone is interested), Sneaking, and Tech stuff. Im sure there's stuff I forgot that should also get cool new stuff. Point is, being an adept should not be about getting the biggest numbers, but about getting to do stuff within that specialty that you can't do elsewhere. Leave the big numbers to people who don't have magic.
-Mages have very little to spend nuyen on, and should have more options for money expenditure that do not include also spending karma.
-Hermetic Mages and Shamans are too mechanically similar, and should have starker differences.
-Summoning is too powerful, letting a single character control multiple creatures that are close in power to another runner. Summoning should be nerfed in some way (possibly tied in with separating Hermetic and Shamanic style mages)
Hacking:
-Hacking feels like a side adventure only one person can participate in. Other party members should be able to take part in the matrix game, or hacking should go much faster. The actual act of hacking can remain the hacker's province, but when the IC attacks and matrix combat is underway, other party members should be able to contribute meaningfully, rather than relying on the Hacker plus the hacker's IC.
-There is no need to use a datajack, because Trodes do what they do but better.
-Programs are cumbersome, expensive, and confusing. The vast majority, if not all, of these need to be cut. Any remaining programs should be in the form of suites, or cheap programs that provide small bonuses. The big cost for getting into hacking should be skill and suitable hardware.
-The Matrix needs to follow the same rules as the rest of the game. Skill+Attribute. Your program might provide a bonus to that roll, but no you can't just replace the attribute with your program. You want to be a badass hacker, you're going to have to spring for some logic.
-Technomancers need to be simplified as well, both streamlining with the new matrix rules, and just being less of a headache to run in general. Removing most programs (and thus need for a lot of the CFs) should help a lot with this right from the get go.
-Rigging needs to be streamlined/improved as well. Currently, it is wholly possible to lose dice on some tests when jumped into a drone vs remote controlling it, which is retarded.
Gear:
-Vehicles need to be streamlined
-Drones should be limited for similar reasons for Mage summons.
-Armor needs to be normalized, with a higher limit for low body characters and a lower limit for high body characters. Characters should not be running around with more armor than a tank.
Misc:
-Hardened Armor should provide free damage resist hits rather than being an all or nothing defense.
Major things in there that I don't think have been covered exhaustively here so far:
-Limiting Summons/Drones in a meaningful way for runners. Having them as challenges is nice, but runners who have an army of drones/summons to throw at a problem trivializes the existence of actual characters.
-Magic should be more about doing cool things than big numbers. Especially true in the case of Adepts. What annoys me most about adepts is they're basically there because anyone not below 1 essence would be better off with Latent Awakening, getting adept, and picking up 2-3 ranks in improved ____ ability. Adepts should not grant bonuses to skills, and should instead provide new options. So mundanes are more likely to have higher skill (due to having nothing else to sink karma into), while adepts are getting neat tricks that let them do new things a mundane couldn't justify doing.
-Combat Skills are heavily overpriced, and need to be condensed to be more in line with the skills available to others.
-Runners should start with baseline competency you'd expect everyone to have. The average person has 3s in all stats, at least a little social skills, and at least some matrix skill. All runners should have this as well. There can be negative qualities to buy these down for people who have it as a part of their character concept that they are bad at those things, but your average person should have them. With the system as is, it's almost certain a new player won't be aware of the importance of these skills, and won't grab them. A veteran might be aware and choose to ignore them in favor of heavy specialization. I would argue in favor of giving 1 free social skill level per point of charisma, with the ability to spend 1 point for a specialization (so a ganger being built with 3 charisma could start with Etiquette (Ganger) 2(4), and at least roll a few dice on social tests.
