I've had several E9x cars, they're pretty great. However, even though I'm in a grassroots motorsports forum, I've never tracked or autocrossed an E9x car before. With that said, I've got a lot of ownership mileage on them and they've been pretty great cars. They have the typical BMW oil leaks, disintegrating bushings, and fast-wearing shocks, but they're overall pretty reliable. You'll need a good BMW-specific scanning tool, there are "shadow codes" that won't throw a check engine light. There is some freeware you can download off the internet (search for "BMW standard tools") and there's also some stuff you can pay for (BimmerGeeks Protool) that's a bit more user friendly. Use this reader to look for codes related to the water pump--its really the only thing unique to the E9x that will strand you. Its electric, and usually lasts ~100k miles or so. When its dying, the fan stays on continuously, so if you test drive a car and the fan comes on at startup, make sure you look for the waterpump/thermostat codes. When you're changing the water pump, swap out the hoses too, they're not long for the world by the time the waterpump is dying. I also ham-fisted the radiator and cracked the radiator end-tank while changing hoses a couple years ago...so I basically replaced all of the cooling system in one go.
As for the oil leaks, look at the intersection of the oil filter housing and the block--that's the most common leak and really the only one that you need to address fairly quickly, since it will leak onto the accessory belt and kill it. The valve cover gasket will leak too, about every 80-100k, and the manual cars have oil pans that are steel and like to leak, though you really don't need to address the VCG or OPG immediatly. FWIW, E46's leak in all of the same places.
As far as selecting a car, go RWD only--the AWD models got a bit neutered with crummier front suspension, slower and heavier steering, steel subframe and a weird transmission mount that makes the manual transmission shifter feel bad. Sport package gets you nicer seats and lower springs. All of the E90 M3 control arms swap into the regular RWD E90s, though it'll probably bump you out of your autocross class, not sure about the rules there. The xenon headlights are dramatically better than the halogens, but they're just okay compared to modern LEDs.
For the comparison of E46 to E90, I'd say that the E46 is more fun than the E90, but the E90 is a better car. Its quieter, just as quick, gets better gas mileage, real people can fit in the back seats, its got a better stereo and the subframe mounts don't tear out. It feels bigger than the E46 though, even if by modern standards its tiny (seriously, I can never find my car in a parking lot, its at stock height and is still shorter in length and height than a Corolla). On the E90s for some reason they added some steering damping to the rack, I guess to make it feel more "high end", so the steering doesn't pull back to center as readily as on the E46s. Its still dramatically better than modern cars. The AWD cars have an even more damped rack though, just another reason to avoid xDrive. The E46 interior looks nicer when its in good shape, but the E90 interiors hold up better. Neither hold up great, soft touch was super popular in the late 90's to 2010s and they peeeeeel.
Anyways, that's my stream of conciousness about the E9x cars. I had a 2006 model 325i sedan for 6 years with the sport package and manual, then an 2011 AWD/auto wagon, then an 2009 AWD/manual wagon, then my current 2009 RWD/auto wagon that I've had for 4 years. I wish I had kept the sedan, it was my favorite of the four I've owned because of its options, but the lure of "practicality" was calling me. It was silly though, the wagon hatch is tiny and while there are certain things that fit better in the back of the wagon, I'd get a better optioned sedan over a poorly optioned wagon any day of the week, especially with the (still) crazy car market. I've focused a lot on the problems in my post, but I really enjoy my car. I've flirted with the idea of getting rid of it, but I just don't know what else would have the same combination of fun, efficiency and interior room at a reasonable price.
