It's rare I'll flat out say "no" to something. I'll allow almost everything and anything, but there are some caveats that I make sure I'm upfront about.
1) "Equal Response".
I like combat in my SHadowrun games. I told someone not long ago that I firmly believe that to most players, whether they will admit to it or not, in their head they see Shadowrun as that scene from The Matrix, where Neo & Co "sneak" into that Office Building loaded down with guns. That said, don't expect to be lugging around giant assault weapons willy nilly.
When I plan out a session, I plan for X Amount of challenge. And X is fluid. If the PCs are all packing little more than Pistols and Armored Long Coats, I balance the opposition based on that. If they have layered form fitting armor underneath armor jackets and assault rifles with APDS or EX EX rounds, I plan around that. What gets the team in trouble is when one or two players steps outside the group party balance and decides he wants to start playing rough. When 4 or 5 characters are in light armor and small arms, but one guy starts kitting out heavy arms and armor, that throws off the party balance, and means I have to plan the bad guys accordingly. Which means the other players either have to step it up or the one player needs to tone it down.
To put it simply, my rule is "If you have it and use it, they can have it and use it". When appropriate. Just cause you own a sniper rifle doesn't mean the gangers will always have snipers aiming at you. But if you're bringing assault cannons to every firefight, more often than not the enemies will have appropriate responses. I like my games cinematic, I run it that way, and like I said, I'm upfront with my players about it. So there's generally no complaints. They know that if they want to escalate the game, they can, but it's not going to make things any easier.
(THat said, there's also a certain logic applied. A small 6-man local street gangs not gonna have military hardware, for example. And just because you walk into Renraku's HQ unarmored and carrying knives doesn't mean the security guards won;t be packing and armored.

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2) "The world doesn't abide the Strange and Unusual"
Vampires and Ghouls and the like are considered monsters. Many of these creatures have a bounty on their head. I downplay SURGE a bit, so outside of a few very specific locales, if you're a freaky looking Surge mutant, you stand out. I don't usually play up the racism aspect too much for most characters, other than to set certain moods or in specific circumstances where it's plot appropriate. But in my mind, playing something weird, unusual, and that stands out in a crowd is a FLAW, and gets treated as such.
I play very "Mohawk" style, so a little weird is fine, but I generally assume that's more in the lines of personal style. I have a very 80's image of Cyebrpunk and Shadowrun. But if, even after taking that into account, you still stand out. Well, it's not a good idea to really stand out.
3) "Flaws re flaws for a reason"
You don't get free points in my game. If you take a flaw, it will effect you somehow. Color Blind characters will find themselves needing to "Cut the blue wire" or meet the "man wearing the red tuxedo". I'll play up negative social flaws if you don't. If you took the flaws for some free points, make it a point to acknowledge and play with those flaws yourself, cause if you don't, I will.
4) "Be a team player"
RPGs are a group game. They're generally a cooperative game as well. No one wins, and if anyone loses, chances are the whole group loses. So don't be that guy, and don't play that character. It's fine to have your own motives, your own goals outside the group. Just don;t mkake those goals and qualities counterproductive to the group. When you have 3 elves and a troll at the table, don't play the intolerant racist. Don't be an asshole, don't ruin the game for anyone else. Otherwise, you'll find yourself making a new character, or even looking for a new game group, real quick.
Bull