4.6iS is an M62 engine, 4.4i is N62 engine... they each have their own problems, so look out for those... well optioned 4.4 can be almost as loaded as standard 4.6 but there are some little things that you will not be able to retrofit the 4.4 to match the 4.6 - the raw power, the certain powertrain tweaks, like having the front shaft going through oil pan (the gurus here, please correct this statement to reflect the correct info!!) to lower the center of gravity... Some other things you can retrofit, like the silver rings on the cluster, or the ceiling lining, maybe even the vented rear brakes...

some things that you can't easily retrofit on the pre-facelift model (4.6iS), like the front headlights with coronas (hard to open lights), or you can opt to facelift the front yourself, new fenders, hood, bumper, headlights... some options, you can do, like facelifted tail lights... but not the panoramic sunroof... the 4.6 would have only rear air suspension, the 4.4 might have all 4 corners...

I personally would take 4.6 (or, better yet, get a 4.8iS), but that is me... if you go for M62 engine, check on the chain guides, they killed my 4.6iS... i am still crying over it...