I personally think that it's ridiculous that some-one with cyberware that allows them to relay messages to their body faster actually allows them to think and interpret data faster. I wouldn't count meat IP bonuses towards hacking actions.
The fastest way to hack is in hot VR with a simsense booster and simsense accelerator. That's 5 IPs. It represents that people are slower when they're still operating in the meat.
However, I don't let a 4 IP sammy use 4 IPs for hacking actions. For me your AR is based purely on matrix initiative. eg. [houserule=
1 IP: AR w/ No matrixware
2 IP: AR with Simsense Booster / AR with Simsense accelerator
3 IP: AR with Simsense booster + Simsense accelerator]
And that's where I'd cut AR off. To get that 4th and 5th IP you need to go hot.
However, the problem with this rule is that running in AR based only on the relevant matrixware means that you're likely to have your physical IPs different to your matrix IPs.
The solution is to have every matrix action hindered if they're lower than the physical reaction. I'd use DP modifiers for this. If you have 1 meat IP, and 3 matrix IPs and you're running in AR, then in one IP, you can take any phsical or matrix action you desire. However, in the 2nd IP you'd suffer a -1 DP Modifier. In the 3rd, you'd suffer a -2 DP Mod. This represents that if your meat reflexes aren't up to scratch, then things in the real world distract you.
I like this solution, because it means that hackers can now take advantage of AR and its coolness, but if they're slow in the meat, then they lose a few of their hacking DPs. Also, Sams can't utilize their wired nervous system to think quicker, as their matrix actions are limited by their lack of matrixware. Of course, a Samurai can easily pick up a Simsense Accelerator modification and then they've got 2 matrix IPs to use.
PS. If you like and understand these houserules, but you don't want to nerf your hacker/sam too much. Then make his penalty similar to the hacker, in that going over his matrix initiative in actions will incur a DP penalty on those actions, not rule them out.
Example. Samurai has 3 Meat IPs and a commlink with a Sim Accelerator. He takes his third action and incurs a -2 DP penalty, because it exceeds his Matrix IPs. If our Samurai has 4 IPs, he can't use that 4th IP (assuming he's taken all matrix actions in this combat), because AR Matrix IPs are capped at 3.
(-2 rather than 1 because I still feel that meat hacking on your wired reflexes (or move-by-wire, even sillier) is silly and broken. You of course can just use 1
PPS. Yes, I do understand how the Booster and Accelerators work, but I've just houseruled them into AR as well.
PPPS. That wasn't too convoluted, was it?