I think most of the other members here would agree that I'm still somewhat of a newbie, and therefore I really don't have a dog in the flintlock vs. Caplock fight.
So for the original question, let me only answer with my observations over the past few years of shooting muzzleloaders exclusively.
I have had rifles fail to fire using caps on a good many occasions. But I have also had instances where I've had four or five misfires with a flintlock. In all cases, the fault was mainly my own. There are certain tricks that one learns in order to keep his or her rifle shooting consistently, weather percussion or flintlock.
I would venture to say that either are as reliable as you make them, using good technique and learning your rifle in and out.
The original poster should only ask himself, which rifle intrigues me? Both are historical and the many Americans who put meat on the table using flintlocks had sons and grandsons who put just as much meat on the table using percussion.
Personally, I have a hard time owning just one of anything. I suggest that you get a good Flintlock and a good percussion rifle. Each will provide their own enjoyment.
Also, don't misunderstand the guys here who advocate for flintlocks. I think they were mainly answering your question as to reliability, which is essentially what I was trying to point out. Either system can be very reliable if well maintained.
Stick around here for a while, read through old discussions and learn, learn, learn. I think muzzleloading is one of the best pastimes you could choose.