I have both flintlocks and caplocks. I love them all, but all of my deer for the past decade have been taken with flintlocks. My dedicated upland bird hunting is done with a 20 gauge caplock SxS, but when I go for birds and rabbits, I take a flint 20 gauge.
OK so pros and cons....
Caplock...,
PRO... better in bad weather. Rarely a slow ignition (though a hang-fire is still possible). Better quality in the low cost varieties. Easier for some to learn on; simpler system so less variables for the beginner. Will shoot any of the substitute powders as well as black powder. Easier to maintain in good shooting order. Highly durable in some lock designs. 1:48 twist rate is found in many many old roundball rifles in caplock or flintlock, and will also shoot some conical bullets.
CON..., needs caps and if they are in short supply you are S.O.L. Caps are also prone to damage from the environment...even simply high humidity when stored over time.
Flintlock ...
PRO..., bragging rights are better when you take a deer with a flinter, especially in damp weather. Properly working locks are so close to caplock speed that a human cannot tell the difference. A cap shortage has zero impact, and flints NEVER go bad in storage. You need to shoot them often to learn their quirks so it's an excuse to go to the range more often.
CON..., You can't skimp on lock quality as it a more complicated system than the caplock, so prices for good ones are higher. It is possible to get a slower than normal ignition, and a misfire can be more common. NO substitute powders for the ignition in the lock... black powder only, though you can use a substitute powder for the main charge. Damp weather will mean special attention to the lock. You need to shoot them often to learn their quirks and if you can't go to the range several times a year, you might have difficulty in the field. They are HIGHLY ADDICTIVE and you have a tendency when you fall in love with a flintlock rifle or gun, you rarely if ever go back to any other form of taking game, caplock, modern, or archery...wait maybe that's a "pro"?
LD