We had a 2005 E53 4.8is. Incredibly awesome vehicle but the maintenance costs were insane! after 20k in repairs, we sold it.
Plan on maintaining everything that goes wrong on an e46 and then some.... cooling system & expansion tank, front bushings (same type of fluid filled bushings that are on the e46 just in a different location), window regulators, motor mounts, subframe mounts, CV joints, fuel pump, etc.
The latch on the back window will go, that's about $250, Ignition switches are prone to failure. There is a gear in the transfer case that goes... when that happens, you have to replace the whole transfer case. You have a 3.0L manual so you'll avoid the failing auto transmission and leaking valve seals, leaking Alternator bracket (yes there is oil going through the alternator bracket) and the leaking coolant tube under the manifold among other issues that the V8 auto have... and you won't have to deal with the crappy air bag suspension either but you'll have the same issues the E46s have: leaking valve cover, leaking OFHG, VANOS, DISA, CCV, etc.
Check the wear on the back tires. If they are worn on the inner edge, it needs upper ball joints... not an easy or inexpensive job.
On the other hand, If it's been well maintained and some of the issues that I mentioned have been addressed then you might want to take a chance. The big plus is that it has the 3.0L and the manual...
I'd recommend hanging out on the e53 section of Xoutpost.com. Thee are a good group of people over there and the posts will give you an idea of what you're in for.
I know the e53 pretty well so feel free to contact me with any questions...
Dinan CAI &Throttle body, ESS Tuning TS2, Bimmerbrakes gen3 headers, UUC SSK & DSSR. Achilles oil pump, VAC oil pan baffle
M3 Motor mounts, UUC Trans mounts, Modified clutch style LSD 3.15, TMS front subframe reinforcement, Koni Yellow sports,
H&R sport springs, UUC sway bars, BMW Perf. Rotors, UUC SS brake lines, Hawk HPS pads, CSL replica wheels,
Rotora strut bar, FXR HID conversion, M3 Mirror conversion, BSW stage 1 speakers