So, after talking to Marcus, it appears to be there. It just isn't all that easy to find and the terminology mixes things up a LOT. But, it is a LOT more flexible with a lot more options than before.
When you create a shared choice, there are two ways of creating them (actually three, but we don't deal with text inputs in this case). You can create a Product Choice or a Product Modifier. In BV2004, there was only 1 type that allowed you to specify a choice along with also being able to modify the price and shipping (or the weight, I can't remember right now). This is split apart into 2 selections in BVC5. The first one is a Product Choice (3 types). A product choice will only allow you to specify an option (like a color) and that is ALL. A product modifier will allow you to specify the choice as well as modify the price, etc. Unfortunatley, if you use a product modifier shared choice, you canNOT track individual SKUs.
So, you can setup a plain Product Choice shared choice and then assign it to a product. (One new thing is being able to deactive a particular choice within a shared choice list on a specific product, which is a nice new option.) However, when you click the inventory you will see very little that can be done. All of the choices will be split out on the inventory window, but they won't have your SKUs on them. All you will be able to do is input inventory and set an out of stock level. (You have to enable them to even track inventory first.)
Where you get to the rest of the stuff those of us familiar with BVC2004 are looking for is under the Product Variations link. Not only can you change the price, weight, and SKU at this point, but you also have options we didn't have before to change the product name, images, long description, and short description. So, you can still accomplish a product modifier as a shared choice while also being able to track individual inventory, you just can't specify the modification within the shared choice - it has to be done within the product once you have assigned the regular Product Choice, Shared Choice.
However, the inventory doesn't appear to do anything at all. Sure, it debits when an order is placed. Any inventory that is in pending orders will show up in the reserved column (this is a nice new addition). But, it doesn't matter how much you debit inventory or what the inventory levels are, it will never display a message on the website that a product is out of stock. Yes, I've set it to "Show as Out of Stock (Allow Orders)". So, I'm not really sure what the Out Of Stock entry in inventory is supposed to do - trigger an out of stock e-mail or show the product as out of stock on the website, because even when I have zero or negative inventory, the site still won't show a product as out of stock.