I've heard the same as Makeitfit regarding the chassis and certainly I had a good look at mine when inspecting and still have a good look if i'm underneath it for any reason.
At the age you're looking at I would DEFINITELY avoid a 3.0 unless it has had an engine rebuild - it's the early ones that have the bother. Consensus is 2003 on (when they changed the engine design) should be pretty much a safe bet as long as you don't mess with the engine ie. EGR blanking/ larger exhaust etc OR if you must mod the engine then you should install things like boost and EGT gauges so you can keep an eye on whats happening.
Far as I know the 2.8 engine is thought to be pretty reliable, just watch as it's a timing belt rather than a chain or gears. Due to the weight of a Y61 (2.5t+) I believe it can be a bit numb at times but then again you are much freer to mod it.
You won't regret having a Y61, I adore mine (sad I know). Very very capable vehicles and should come with rear diff and rear arb disconnect as standard so can handle whatever you throw at it plus she's live axles front and rear. Towing limit for the 3.0 manual is 3.5t (2.5t for auto) and I think it's the same for the 2.8. Either way they are capable of towing and handling far more than they are rated for.
Only other cons I can think of are that I think you are early to mid 20s for mpg (slightly better with the 3.0) although that was never a factor in my decision to get one.
Biggest con is you can't get a 4.2 diesel Y61 without importing!!
(I'd even go with a non turbo one...)