I have shuttle, HST, and gears.....and think we have had every transmission made over the years. Frankly, we haven't had any problems with any of them.
I replaced one dry clutch in a manual transmisson JD with over 10,000 hrs, a shifter bushing on a Yanmar, and nothing on any of the others. None of the jobs was major.
It comes down to your primary use. If you are doing a lot of loading or detail landscaping or lots of back and forth like cleaning stalls with the front loader, then HST is far better. Convenient and fast changes in direction are what HST excels at doing.
Anytime you are going longer in one direction - like bushhogging, field mowing, or grading, then the shuttle gives constant speed and a quietly efficient ride with way less operator input.
An advantage to the shuttle is that it is often paired with a lot of separate gear ratios, making it an 8 or 12 speed. The HST is variable ratio so it covers a similar ratio range, but is definitely less efficient. Most of the time the efficiency doesn't matter because you make up for it with more throttle. You will notice the lack of efficiency more at very low or very high ratios.
My experience is that shuttle transmissions tend to be quieter than HST - which does have a characteristic whine.
But either one will do both jobs.
rScotty