A 2000 will be a facelift, hence 2.6l or 3.2l, IIRC; I choose a 2.6v6 but a lot of the fans (
www.cavweb.co.uk) reckon it's better to hold out for the 3.2 (more power, not significantly less mpg).
Gearbox?, depends very much on your driving - lots of town traffic and the (very good and smooth) autobox will make your life a lot more pleasurable; I was very hesitant about changing from a life of manual boxes to an autobox but have never looked back. You will find, however, that the higher spec'd Omegas, especially the facelifts are mostly autos. If you particularly want a manual then look for the superb MV6 variant, just stay away from ex-plods (or look at them with eyes-wide-open).
Get used to pitiful MPG if you do a lot of short journeys - the Omega is fantastic when its out on the open road but very thirsty around town.
Lastly, consider CD / CDX / Elite specs - you get a lot of gizmos for your money. Just remember to check them out before buying - check seat electrics, in particular (heated seats and position / height adjustment)