HI,
1. I don't see what you mean. While the cart view of the checkout do uses a table, that has always been the case since HikaShop 1. And that's the same for the payment and shipping selection views.
The rest of the checkout doesn't use tables. Before HikaShop 3, the user registration form was using a table and with HikaShop's user registration form, there is no table anymore there, so I would actually dare say that there are actually less tables with the new checkout.
Now maybe you had someone customize your old checkout to have divs instead of tables everywhere. If you want to revert to that then turn on the "checkout legacy" setting of the HikaShop configuration and you'll be back on the old checkout of HikaShop 2.
2. That's because the quantity input view was changed with HikaShop 3 and the customization of the view that you had in place for HikaShop 2 is not compatible anymore with the javascript of HikaShop 3. You'll have to revert your customization of the "show_quantity" or the "quantity" view file via the menu Display>Views by clicking on the "remove customization" in order to get the default display of HikaShop 3.
Note that there is now a "quantity input method" setting in your HikaShop configuration that let you choose between different looks for the quantity selector.
3. Similarily the cart module has been customized for HikaShop 2. You'll have to remove the customization of the file "cart" of the view "product" to go back to the default display of the cart module of HikaShop 3 and it will work again. Then, you can reapply your customization to that view file.