It really boils down to how much are you willing to spend and what do you want cosmetically. I think that custom bows are beautiful with fit and finish that can't be competed with. The idea of being able to get the exact weight at your exact draw weight with the exact woods you want with a grip that is designed for your hand (big, small, low grip, high grip, etc.) is what draws most of us to custom bows.
The mass produced factory bows, from reputable companies like Bear, Martin, etc. will shoot well and last as long as a custom. They will usually cost less too. The won't however be any different than any other bow of the same make and model. There are thousands of Bear Montana longbows out there. They all are the same. With a custom, you get a "one of a kind" handmade bow that is uniquely yours. You can find a gazillion Brackenbury's, Blacktails, Black Widows, etc. out there, but you won't find two exactly alike. The customs are one of a kind works of art. That is big medicine to most of us. If you are not into that, or are on a tight budget a factory bow will serve you well.
If you are looking for a R/D longbow, I recommend a Toelke Whip. They are beautiful and as smooth as any recurve I have ever shot. I am sure that there are other custom bows out there that are as just as good, I just haven't found one.
I think that whatever you choose, shoot it lots and you will be happy. The bow is only as good as the archer holding it. Find one that gives you confidence and shoot it until you are accurate. Don't feel pressured by the lure of custom bows. If you order one, you will love it. If you don't there is no reason you can't shoot just as well with a Bear Patriot or Bear Montana. The deer won't know or care what kind of bow you shot it with. The taking of an animal is a privelege and can be accomplished only through dedication and hard work. It absolutely CAN'T be accomplished by dumping $1200 bucks on a custom bow.
Good luck with your quest for a new bow. The beautiful thing about it is you can't go wrong. A bow is a magical thing and will give you years of happiness. No matter what bow you choose.