They are both solid engines, the 2.0 16V unit is very well known and it's widely regarded as a solid and dependable engine, the V6 looks more scary for the uninitiated but it's quite a simple engine and despite it's dubious origin from the good old US of A it's an equally dependable and simple engine. There are no horror stories attached to either of them, both of them perfectly livable-with and robust power units.
But it has to be the V6, there isn't a lot of difference in value between then, the VED is identical for the majority of them and what you loose in a few MPG you'll gain back in a fair bolt of torque and a muted but nice V6 sound. Depends of course what you're after the Zetec at full-tilt sounds like any other fizzy 16v four-banger, the V6 sounds the part wide open and treated gently won't be far behind on MPG, it works considerably less hard during cruising.
I've not driven a 16v Cougar but I did have a 2.0 mk2 Mondeo and whilst it was perfectly adaquate performance wise 95odd bhp/tonne isn't going to slap a massive grin on your face, it's perfectly drivable though and will keep pace with traffic.
The 2.0 16V is a belt driven unit, the 2.5 24V is a chain driven unit, chain failures are vanishingly rare, that said so are "within schedule" belt failures. The wobbles that'll finish off a V6 thankfully tend to claim them fairly early on so a car that's still running x-years later will probably be beyond the worse mechanical failures.
Don't fall in to the trap of thinking a Cougar drives like a larger Puma though, they handle well but they're a comfortable GT that'll make good progress around the lanes, they're not a chuckable "hooligan wagon" like the Puma.
Avoid the automatic would be the best advice, the C4DE is notoriously problematic and you'll need a calendar to calculate spirited runs.
