Yeah but there is something to be said for the smoothness and sound of a V6. (Says the guy who is pulling out all the stops to bring home a V6 car that seems to be having at least some of their typical issues....
, as OH said above the Euro spec 2.5L V6 TDI engine is known for having some trouble areas (injection pump and valvetrain primarily). But its advantage (though I realize this is not the answer to the question you asked) is that in other markets it was available as a factory option in the C5 cars. So if you wish to go to a 6cyl they are the most obvious path. No reinventing the wheel in terms of electronics, fitment, plumbing, transmission interface, etc. Can't say what exactly those aspects would look like with the 3.0L to a C5 but it is a safe assumption that they would be much more challenging, presumably solvable with enough skill and effort and funds but not easy.
The 2.5L engine's downsides, aside from those couple common problems, is of course acquiring one in N America, and then sourcing parts from overseas to keep it going. But to me those are livable downsides for a car that is not my primary vehicle and thus it is the path I am taking with my '01 C5 allroad. I do know of a couple more 2.5 engines with harnesses that are available if you are going to look into that route and want to PM me.
Plus of course the old 2.5L is smaller displacement and much more primitive technology than the modern common rail 3.0L engines we got in the US, and the 3.0L's power and torque figures simply stomp all over the 2.5's. And you get US dealer parts support from VWoA on the 3.0. But again, for any of those factors to even matter at all in a practical sense, you'd have to be able to successfully install and integrate it in the C5 car. No small challenge. I think Scott DeWitt on here tried a swap with a 3.0 in an allroad years ago, and to my memory, he did find a clutch/flywheel recipe that went together OK and managed to get the engine sitting in the car. But his thread eventually petered out and my suspicion is the swap never reached the road due to trouble with the details.
Oh yeah, the other downside to the 3.0L of course is that it is extremely complex and has timing chain issues, can have the usual CR fuel system failures, etc. The 2.5L V6 is a belt motor with an old school rotary injection pump that does not suffer those.