Well if we speak about primary and secondary for fun i would say blacktail/bolt action sniper...sometimes i like to go TMP/BLACKTAIL/KILLER7...but to answer your question though! TMP/SEMI AITOMATIC SNIPER/ STRIKER
Ohhh depending on my mood I will use either the standard Handgun or the TMP - that 5x critical rate on the Handgun's special is no joke. It obliterates things, including plagas. The TMP is nice for ammo capacity, speed, and stability. You can place very deliberate shots - stun enemies, hit legs for suplexes, and it doesn't ever feel like you're wasting ammo.
I use the Riot Gun because it just seems to do better damage and criticals from further away. You also get it earlier - I don't like waiting until chapter 4-1 before feeling comfortable to upgrade a shotgun.
I like the bolt action for delicious animations and that special upgrade that basically puts it on par with a magnum. The pausing to do the bolt action between each shot can seem annoying at first, but I like the fact it pulls the camera back so you can quickly check your surroundings before taking another shot.
Everyone says the Broken Butterfly is the best magnum but it only overtakes the Killer7 right before the final battle (when you get the special upgrade). I don't do NG+ so I stick with the Killer7 every time.
Standard handgun: fully upgraded to 5x crit is a no-brainer. Standard shotgun: fully upgraded to do max damage at all distances? Also a no brainer. Bolt Action Sniper: fully upgraded does more damage than the semi auto, plus it forces you to carefully pace yourself between each shot. No brainer... to me at least