You know, if we really don't like the changes in SR4A, if we put together some kind of standardized set of house rules as an alternative, there's a good chance it would become the "standard alternative". So lets compile a bunch of suggestions, and I'll take them and write them up and do some kind of pdf once things are settled a bit.
So house rules I've seen that sound good:
Overcasting: Overcasting causes Force + modifier physical drain (not F/2 + mod drain) or Spirits Hits * 4 physical drain for conjuring tests.
Direct Combat Skills: Ignore the extra drain in SR4A.
Physical Illusions: Must score successes greater then the sensor rating of the equipment to be fooled (not the Object Resistance of the object, a simple device made out to steal is not harder to fool then complex electronics).
Upgrading Equipment: Equipment comes in two types module and non modular. Non modular equipment is not met to be upgraded and is subject to the +2 limit. Modular equipment is made to be upgraded but (I am so completely lost when it comes to matrix rules that I'm not sure how to say, you will need to replace hardware). Comlinks with system of 3+ and drones with availability of 8+ are considered to be modular.
Karma:
Skills cost New Rank * 1 to improve.
Skill groups cost New Rank * 2 to improve.
Stats cost New Rank * 4 to Improve
Stats over Max for their metatype cost New Rank * 5 to improve.
When improving a stat either add or subract the amount over normal minimum/maximum of the meta type (for example a metatype with 2/7 willpower going from 2 Willpower to 3 Willpower would be treated as going from a state score of 1 to a score of 2, a metatype with 1/5 willpower going from a stat score of 1 to a score of 2 would be treated as going from a score of 2 to a score of 3.