Skid Steer Disadvantages I've experienced (Had a Skid Steer for the past 20 years, and tractors my whole life - 50 years):
1. You mentioned it, ground clearance & also muddy ground, or non-flat terrain
2. They suck for digging holes. OK, you can rent a backhoe attachment, but they're a pain IMO. Tractor is better for digging.
3. Tires. They go through tires like a stoner goes through Doritos. OK, not that often, but I'd say we replace tires every year and half or two on the JD 240 Skid Steer, but the Kubota M6800 tractor is 20 years old with the original tires.
4. Towing or plowing
5. Hard to use in the yard without causing damage.
6. Harder to work on. There is so much stuff jammed into such a small area that it's hard to get to stuff to work on it.
If you are OK with those things, they're better at everything else. If I could have only one or the other, personally i would choose the Skid Steer. The versatility & number of attachments you can get for them is staggering. If you live in a snowy area, they absolutely rock at moving snow, & you can get a plow for $500-$600, cheaper if you look hard for a used one.