Ive had two BMW's with M62 V8's (My 4.6is and an E38). I personally think that the sporty, yet slightly muted sound of the M62 is one of the best around. It's also got to be one of the smoothest V8's available, especially when compared to a Merc. I have drivin quite a few E53's with the M54 6 cyl and I wouldn't say they're by any means slow, just not near the same driving experience. The GM transmission in the 6 cyl version is obviously geared to haul the weight. One of the turnoffs to me was that the 6 cyl seems to be constantly shifting even at normal driving, and most of those shifts are happening around 3k rpm. The V8 is extremely flexible as it will lug along at 1500 rpm or scream to 6800 with plenty of torque curve inbetween. The M54 gets most of its power at the higher end of the rev range which is great for an E46, not the best for a pig like the X. Again, simply my .02 here.

As far as reliability I would say the M54 6 cyl is probably less maintenance overall as theres only one valve cover and that itself is much less labor to replace. No valley pan; a common M62 leakage area which requires removal of intake, water pump etc. Most of those cooling sytem parts are much less work to replace as well on the M54.

The M62TU in itself is a wonderful engine in my opinion. It seems much less affected by overheating like the M54. Its just the cooling system and rubber parts around it that seem to have a relatively short lifespan. I've seen a few of them with over 250k myself, as long as the cooling system is kept up to date and engine is kept sludge free and clean internally with on-time oil changes. I dont know of any bottom end or internal failures with either engine unless they're just mindlessly abused.

I would drive both and just use the "seat of the pants" feel. Let us know what you decide