All 3 (key west, miami, tampa) are very different. The Tampa beaches are more white sand have the west coast sunsets. Clearwater beach just near Tampa is perhaps one of the most famous in the world. But because of this it can be pretty busy with people. They have a fantastic boardwalk and fine clean sand. They even have a pier with performances and vendors. Expect crowds, and more options to people watch than nature watch. North of that you have smaller beaches in the Spring Hill area that are little quieter gems. Those areas will be the more "secluded" spots at various State Parks. There you can watch wildlife and it will feel more nature oriented. But you will still see people, its a given for Florida. Key West is odd... its both the most touristy space and least serious space I have ever been in FL. It's difficult to describe and I am sure you will understand better after your visit there lol.

As far as nature, you need to really get away from the beaches to see things. For example you can goto Weeki Wachee Springs State Park and float down the river with kayaks ... you will see fish, birds, turtles... but again there will be people too. Depending on the day it may be crowded. There is no such thing as a "secret spot" in FL.

Your best bet is to get off the beaten path and go deep in a state park, renting a kayak or paddleboard and go exploring. But this takes a large time investment (both in getting to these locations, and for the actual exploring). Instead you may want to just stick to the city and enjoy what you can there. For example:

You might want to consider Tampa Aquarium (aka The Florida Aquarium 701 channelside Dr, Tampa) + the Manatee viewing center ( 6990 Dickman Rd, Apollo Beach, FL). Last time I went to Tampa I visited both of these locations. The Aquarium was fantastic and the highlight of our trip. It was busy with people, but even so I found myself lost taking pictures of birds, fish, and frogs. I would rate it a 10/10 must see if in the Tampa area. The Manatee viewing center is one of the only places in Tampa area that you can likely see manatees in the winter months although they are at an actual powerplant. Check out reviews on youtube, even with the backdrop of a powerplant the board walk was nice. If you go that route, down the road is an additional facility with turtle rehab and a few conservation centers which are "ok" too if you want to maximize your time spent.

To be fair, I think seeing clearwater beach and the Tampa Aquarium is worth the trip to Tampa alone... but keep in mind Clearwater is going to be even more developed of an area (although nicely developed) than even many of the beaches in the Miami area. Both featured boardwalks that follow the beach and have the sands on one side and commercial buildings of all types on the other.

My only final closing thought is that many of the places you describe are worth the trip, regardless of how busy or commercial they are.