Reviving an old thread for anyone interested in continuing this discussion.
Reasons I bought my RS4:
V8
Manual
AWD
If any one of those don't matter much to you, the E9X is probably the better platform (I've owned two E92 M3's). The E9X handles better, but I do enjoy the endless traction in the RS4 too.
The downsides have already been discussed but here are the big ones:
Carbon buildup
DRC (suspension)
A lot has been said about the carbon buildup, but at the end of the day, the impact to this is performance, not catastrophic failure, so don't let this be a deterrent. My car went 90k miles without a carbon clean, I had it done, and now is back to like new. Timing chain as mentioned earlier is a fault with the S4, but not with the RS4. For me, the rod bearing issues with the M3 were a much bigger (and expense) concern than anything engine related in the RS4. Especially as these cars begin to age. For those unaware, the same version of this engine was used in early R8's.
DRC can be hit or miss, but you're looking at ~$2k to remedy with coilovers, not too bad for a German car.
Additionally, the infotainment system is very dated compared to the E9X, and there are less features like hill assist, or the ability to maintain cruise control while shifting between gears. Little stuff, but still a sign that one car (E9X) was at the start of its lifecycle and the other (RS4) was at the end in 2008.
At the end of the day I needed a car that could safely take me up icy mountain roads, hold a couple kids, and put a smile on my face. Check, check, check! Car is now 13 years old, and I can honestly say it rattles less than my brand new M2 did and sounds fantastic. I would say it's worth a look if you're in the market for something similar. Not a lot of cars for sale today that comes close.