The major changes I noticed between the two editions are as follows:
Limits prevent characters from being overly min-maxed. Each of them is centered around an attribute that is typically dumped in normal characters; the most important attribute for the physical limit, for instance, is Strength, though other attributes weigh in they have the same impact as Strength does alone. This means that you can't build a "never gonna fight close quarters" build and just dump strength and expect to do well in other physical areas, encouraging a well-rounded thing.
Mystic adepts get a huge buff. I'm not exactly sure that this is a bad thing; they still can't astrally project, but they get the powers of both mages (other than astral) and phys-ads pretty nicely. Were they still using the BP system, this would be a flaw, and I'm not sure about allowing them as the third pick on your priority system, but I think the reason that people are upset is because they don't astrally project as much as they should when not a mystic adept.
The priority system really makes things a lot better. It prevents some of the worst cheesing during character creation (don't get me wrong-it's still possible, but you have to know what you're doing and make some sacrifices).
Combat's been changed rather heavily on the bookkeeping, but not so much the execution. The Accuracy limit keeps pistols from killing Great Dragons, which is a nice touch, but also discourages just dumping into the newly increased skills and maxing them out right away. It also makes smartlinks a more tangible advantage, as do laser sights. Armor is now a single rating for stun and physical, which makes it a lot easier for new players to understand, and, in my opinion, more realistic.
Hacking's a lot better. Mind you; the wireless thing contains some logic holes and gimmicks with the new benefits it gives stuff like cyberware or laser sights, but hackers can enjoy a target rich playground with new rules for hacking that make prepping a hacker 90% easier and playing one about 50% easier; GM'ing hacking also became a lot easier. In addition, some of the more broken technomancer stuff has been revised so you now have a reason to play a decker instead of a technomancer every single time.
All in all, it's faster and more streamlined. If you want my "reviewer" version, you can check it out on my blog, but I've said pretty much everything I said there here, only without the sales pitches.
Helmets can be modified to include vision and audio enhancement. The full body armor's helmet for instance have a capacity of 6 (which is appreciable).
4th edition had a rule for targeting a spot not covered in armor and I think it's still valid and interesting in 5th edition.
Target an area not protected by armor. The attacking character receives
a negative dice pool modifier equal to the target’s armor (better
armor is more difficult to bypass). If the attack hits, the target’s armor
is ignored for the damage resistance test; the target rolls only Body.
This way having a full armor with a full helmet would makes it (almost) impossible (-18) to do. Which makes sense to me. At this point I would probably just call a shot to the head and hope to pierce the metal.
This is only if your GM is using this rule from 4th edition (which I expect to see back in the Arsenal book eventually).
Like Scrollmaster mentionned, there's also the fact that helmets masks your face but it's probably not suitable with some dress codes. Don't try to get in Dante's Inferno with anything else than a nice suit or dress.
Best Answer
First, no. There is no good, hard rules on adding negative qualities during game. There have been suggestions and precedence that have been set by Addiction rules. But, for the most part, it's up to the ST. Because of this, I can't really give you a RAW explanation of what to do.
However, I CAN give you better on your second question.
I've had a number of games in my campaigns where I've added negative qualities for things that players have done during the game. A few times, it was addictions. But one of them was an Enemy. During the game, the runners had been sent against a corp executive that had some information for their actual run. While doing the run, one of the players thought it would be a good idea to blackmail him. I had let the player know that this guy was a pretty high-up executive and blackmail wouldn't go over well. However, they continued on with their plan. It had succeeded, since he had a good idea about it. However, the blackmail data had been caught by a rival group that wanted to deface the exec. In short, there was a fire fight and some fun with jumping over moving cars. In the end, one of the group had gotten away with the blackmail data before the runners could give it back to the exec and the exec escaped.
Now, the one that had been doing most of the blackmailing and talking has a corp executive with a lot of resources wanting him dead. What does this mean? No more taking runs from this corp...and sometimes, they would have to deal with a group of runners or corp security as a distraction during other runs.
The player liked the idea and took the negative quality. And, after a while of having runs sometimes go pear-shaped because of a group of newbies wanting to cash in on the bounty on the one runner, he finally paid up on the negative quality and I gave him the chance to eliminate the exec.
In short, negative qualities are something that you can add to players that will give them different hurdles for doing things half-assed or screwing up. And you still give them the ability to use Karma to buy the negative quality away. But I wouldn't constantly do it. Once ever three games, and only when they really deserve it, seems fine. It's not so much that it would make the game more gritty. It just makes it kind of unrealistic to carry around that much negative baggage. If they earn it, they earn it. But I wouldn't slam with it too much. And you shouldn't reward them with Karma or give them more for giving them the negative quality. They earned it from doing whatever got them the quality.