He lives!! I was wondering about you
I do agree Astral Perception needs to be fixed. Right now it's better called Astral Vision, which is an early assumption I'm not sure we should make. I don't think it should go quite as far as you take it, but certainly it needs to be toned down...
-You 'see' everything
This is definitely a problem. It's super vision. The rules in the book need to reflect better that stealth still works against astral vision, even if it's at a penalty, and that all soft cover is completely effective (I would argue, including glass). Astral perception should be more confusing, and I don't see why a mundane standing in an empty room should be like a 'beacon of light'. Magic should definitely be easy to notice, but mundanes should just fade into the background clutter, even if it's in a place without a lot of other living stuff. Perhaps require a perception check to notice anything, even the most basic stuff, while using astral perception?
Related, using astral perception to aim a gun or to sword fight is silly. Again, this shouldn't be astral vision. A +2 modifier is not enough for 'I know there is something alive there that is threatening to me, I can shoot it with my eyes closed with this gun'.
Instantly recognizing auras - This would seem to be a two-sided problem to me. On the one hand, it shouldn't be so completely easy and instantaneous. On the other, it needs to be communicable to others. I imagine that an aura has several 'threads' in it, some which are more or less permanent, some which are very volatile. It should be possible to study the more permanent parts and be able to recognize that signature (using aura reading). There should also be a specialized thaumaturgical language to describe such things to other people, so Lone Star for instance can actually keep some reasonable record of people to compare spell signatures to.
Invisibility and the astral - On this I disagree. All spells should be more or less clearly visible on the astral.
Astral perception being a 6th sense - not sure on this one. In my 'pre-SR' game I'm running, the character was/is psychic, which fed into her being able to awaken before the actual awakening. Certainly they should be related. In the Mercurial adventure, we saw an instance where any awakened character are thrown into an astral vision even when they're not perceiving, so it has canon basis as well. I have no problem with awakened people being subject to suddenly being thrown into visions, feelings, etc. even while not perceiving.
On the other hand, because of the nature of the dual-natured rules, we do need to be able to turn perception off, even if the general 6th sense is still on. When astral perception is on, you're vulnerable to spells from the astral, etc. When it's off, you aren't. In both cases, you're still vulnerable to other 6th sensey sort of things.