I am not sure what other form factors Beratta is making for .40 nowadays
but I have both a Beretta 92FS 9mm and and 96G Centurion .40, I do not notice a hugh differnce in recoil between the two but there is some. Since both of mine are based on the same frame, it is a very similar feel to shoot either one and with the exception of barrel length, they look the same. The M9/92FS has a safety integrated with the hammer decocker, while my 96G has a hammer decocker only.
Assuming personal style preferences for one model over another are removed, I quess some of the factors I would suggest considering for choosing one caliber over the other would be:
1) 9mm is a cheaper round to buy if you go thru alot of rounds at the range
2) If just learning, or maybe a smaller shooter, 9mm has less recoil and may be easier to learn to shoot properly with
3) Both rounds are fine for HD usage but .40 has better stoping power if you are looking for a more lethal version of HD weapon
4) 9mm is a military standard round and very common so if the SHTF and you had to scavange for ammo, 9mm may be easier to find then .40