If you're looking at a car in the changeover period which seems to be the case, I'd strongly suggest that you drive both. I can't comment on the E63 specifically but I have experience with both engines in the SLs and whilst both are good (maybe great?), they are different. Both provide decent performance but I think the 6.2 needs to be 'driven' just a tad more than the 5.5. I suspect that most people would find either to be perfectly agreeable but on balance I prefer the way the 5.5 drives. Only just though and I'd be very happy with either. I have nothing against NA V8s, having a TVR V8 which I've kept for 15+ years simply because I like it and can't really find a decent replacement - the SLs are great but different to TVR and you'll find the same with an E.
I'd also suggest that you check out the slight changes with the dash displays on the E, which changed around 2011 IIRC. Others have mentioned head bolts but there's plenty about it online.
ETA: Thinking about it, as the car is likely to be a few years old, I'd probably prioritise condition, ownership & service history, colour/spec etc rather than holding out for a specific engine
I'd also suggest that you check out the slight changes with the dash displays on the E, which changed around 2011 IIRC. Others have mentioned head bolts but there's plenty about it online.
ETA: Thinking about it, as the car is likely to be a few years old, I'd probably prioritise condition, ownership & service history, colour/spec etc rather than holding out for a specific engine
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