I'm in Ontario, too. My requirements were mostly the same as yours, pest control and some plinking. Although I've ended up inheriting a few other guns, the ones I "chose" as farm guns based on local advice were a .22 and a .410.
If you want to shoot skeet, you'll probably want a bigger shotgun than a 410, mind you, since I think you need to be a pretty good shot to hit a clay with that load. Otherwise, my personal opinion is that a 410 is a good long gun choice for dealing with whatever's in your front yard for someone relatively new to shooting. It's light, low recoil, generally won't penetrate walls but has as much energy at the muzzle as a .357, and doesn't splatter raccoons the way a bigger gun would do. That said, if you're comfortable with it, I wouldn't argue with the 12 gage reco.
Again, my personal opinion, but around here I don't think a handgun is worth the bother for dealing with pests or intruders. The cops deal with incidents involving a handgun entirely differently than they do with a long gun. And if you intend to be compliant with the law, a handgun is all but pointless. You need a transport permit and a locked case for it and you have to be defensibly taking the shortest route from home to range. A long gun only needs to be hidden from sight in a car. Handguns are too much trouble for not enough benefit on a rural property in this country. Note too that if you want to join a local gun club and use their range, they'll generally allow rimfire guns, so you can still work on your proficiency.
As with the previous thread on this topic, YMMV. Just my advice, Canadian to Canadian.
