There are not classified shuttle equivalents launching, not sure what you are talking about there. The X37 has the capability to land, but it is not manned and is tiny compared to the shuttle.
>research that couldn't be done with automation
I'd think there is room for both. Automation makes sense, but don't think the versatility of meatbags is entirely there yet.
A bigger problem is lack of expertise. Astronauts are not specialist in whatever is the topic of the current experiment. You need probably like 5 years of training (assume the second half of the undergraduate degree, and perhaps the first half of the PhD). So experiments must be fully automated except for a button to turn they on and off.
You can send up a lot of less versatile bots for the price of one meatbag.