I currently own a 2.5 and a 3ltr, the 2.5 is a 2000 the 3ltr is a 99, both have done roughly the same millage and untill i fiddled with the 3ltr both were standard.
The second one i bought was the 3ltr kind of says it all.
Both are late engines so have the refinement tweaks that have been made over the years and in the actual 'smoothness' theres nothng in it.
To 60 theres not a horrendous amount in it, but from 50-70 and above the difference is more noticeable, and flat out its 3ltr all the way, it just keeps pulling.
The 3ltr is better to drive with a bit of agression, but then its the MV6 as opposed to a CDX so always will be.
Driven the same way theres very little difference in mpg, 1 or 2 miles at best, but with 2 or 3 passengers and a few bags the 3ltr feels more comfortable in the motorway speed up slow down situations.
To be honest you pay your money you take your choice but as the prices are almost the same a late 3ltr would be my choice over a late 2.5.