I know two different kayaks, apples and oranges, but trying to decide between Native Ultimate FX 12/15 or WS Tarpon 120. Will be using primarily for inshore, flats, and marshes. Paddle trips less than 10 miles. Like the idea of the Ultimate for ability to stand which you can't do in the Tarpon, even though not a priority. Is there a significant difference between these two kayaks as far as tracking or speed. I know some stay away from the Ultimate because lack of scuppers.
Any input would be appreciated.

Yeah very different platforms (totally apples and oranges).

I have a ton of experience with the Tarpon 120 and none with a hybrid style kayak, such as the Ultimate FX.

The Tarpon is a great platform for multiple applications, but not a standing kayak. Not so great for heavy storage, either. Great for longer distance stuff.

The FX will carry pretty big loads, allow for stability and standing, paddle well over decent distances, and offer comfort with the frame seat.

The big difference I see here is safety.

The FX will swamp and take on water if you get in trouble, so make your decisions based on that. The Tarpon will give you more safety.

You don't want to be in the ocean, by yourself, and get in trouble. You don't want to be in freshwater, either, and get in trouble. But, you have to weigh out your "style" with your platform decision.

For example, I fish freshwater exclusively, and I usually stay close to the banks. I wouldn't mind swamping an FX kayak because I wouldn't be in any grave danger.

I've owned about four sit on tops over the years and an older model Ride135 that was super stable.
I've now been fishing out of a Commander 120 and it's a very stable and safe boat.
Don't let anyone scare you away because it doesn't have scuppers. Even if you were to take in water it would take an awful lot to make the boat unstable.
I carry a large sponge to take care of any water that gets in from paddle drip or my feet when I put them into the boat.
I've never gone out in waves that would wash over the side, but I've been in water pushed by 15 mph winds without any problem.
You actually sit lower in a hybrid than you do on a sit on top so the center of gravity is lower thus more stable.
I love the boat and besides the stability the room is second to none.
I would take my kayak anywhere but into the surf for obvious reasons.

I agree, I think safety is not so much driven by the issue of scuppers or no scuppers, but using common sense and knowing the capabilities of your craft in varies conditions and the paddler. When folks find themselves in trouble or lives are lost not an issue with scuppers vs no scuppers, but poor decision making and disregarding safety, ie: not wearing a PFD.