Don't know if you want the opinion of an HST owner (hopefully, we're not disqualified or considered fanatics or something ! /forums/images/graemlins/crazy.gif), but here's my thought.
Seems to me it's mostly a matter of preference, and what kind of use the equipment will get. For true, agricutural crop-related activity, the gear tractor has some advantages including efficiency and precise ground-speed. For utility work and FEL operation, HST is probably more convenient.
I spent many hours on gear-drive IH, Case, Ford and Fergusons in my mis-spent youth, and have some antiques I am restoring, so a straight gear tractor is perfectly OK to me. But, when shopping more recently, I looked at and operated both GST and HST models. Liked 'em both, and went with HST as most suitable for my needs today. It probably says a lot about how these Kubota models are used that so many go with the HST.
For tractor gearheads, the choice of transmissions seems to be a topic that evokes a lot of emotion. I could only guess why this brings out so much controversy /forums/images/graemlins/confused.gif... my guess being that these new-fangled transmissions cost more and it gets to be a budget vs. features thing. In the end it has to be a practical choice for each owner... since they are the ones who have to use their own equipment.
So, if you're trying to figure out what to buy, don't be swayed by the opinions of others or the relative popularity of an option; instead figure out what you will be doing with the equipment, and then choose the option that will work best most of the time and fits your budget.