A flint gun is more forgiving of touch hole location. As long as it's somewhere within the semi-circle of the pan it will work. (There is of course, the "ideal location".) If it's less than ideal (due to liner or breech plug location, the interior of the pan can be filed and altered in order to make it work better.
With a flint gun you only have one machining operation to perform. Installing the touch hole (or liner if you choose to use one--and most people do because main charge ignition is faster and more certain).
The down side of flint is they are slower in their lock time and longer barrel in total barrel dwell time for your projectile, which makes them less accurate in non-rock-solid shooting positions. They are finickier in getting to work reliably. Not any LESS reliable, but there are just more things to have to pay attention to or could go wrong. Usually the fix is pretty apparent (dull or misaligned flint, or clogged touch hole).
The down side of cap guns is that caps are not always in abundant supply. Caps can often burst on the nipple sending little pieces in different directions. You should ALWAYS wear shooting glasses anyway, but the fence on flint guns tends to contain most of the flint shards and directs most of the flash away from you. Flint sends a jet of hot gasses to your side, so pay attention to the guy next to you on the shooting line, or, let him know when you're going to shoot so he can be prepared.
Most all the cap guns that you see have a flint version, as, cap guns really only came in to common usage after about 1820 or so. Many many flint guns were converted to percussion after that time and up until the cartridge era.
As far as which one? That's really up to you. I would suggest you make a list of features you find attractive, (slim / robust overall dimensions, hooked butt, narrow butt designed to be shot off your arm / wide designed to be shot off your shoulder, shorter / longer / mid length barrel, half stock / full stock, straight barrel / swamped barrel, Patch box properties / features, wedges / pins, etc.) and use those preferences to narrow down the search for yourself to help decide what styles you find personally appealing.
One thing about cap guns and the era though; If you find carving (and particularly raised carving) personally attractive, that really went out of vogue during the cap gun era. After about 1820 or so, builders tended to use metal inlays more to decorate their work, rather than using intricate carving as the focal point of their embellishment features.
Engraving is a whole other subject, but most metal inlays were engraved to some extent as well. The certainly don't HAVE to be, but on the finer guns they usually were.
I would suggest going with a pinned gun first rather than one with wedges, because those can be every bit as tricky to get right (actually more so, and there is usually more than one of them) than a cap gun drum installation.
The Jim Kibler kits get very very rave reviews, because a lot of the decisions and critical locations have been done and made for you already. The Track / Pecatonica parts sets leave a lot more work for you to do (and enjoy). The down side of the Kibler kits is that they are very very popular. Slower lead times, and a LOT of guys are building them,(you will still be the "first kid on your block. and neighborhood", but not the first one in town) but still far fewer than the Investarms / TC / Lyman "sand and assemble" kits.