An x-pen is probably cheaper, especially if you can find a sale. There are some disadvantages, mostly that it doens't have a bottom or top, so can be hard to clean and rabbits could jump out. You could make a base using coroplast, or get more fancy with a wooden base. A top could be a sheet, wire mesh, or just using a taller pen. X-pens are nice as they are big, easy to set up, and portable if needed. It you can good to have an x-pen anyway to expand the area, use outside, or for travel.
With a wire dog crate, it is fully enclosed. You can add a shelf to it as well if you want. Fleece or a towel can work as bedding, but rugs or mats can work well too. They are a bit more expensive, but you may find a sale or a used on that would work well. You would want a fairly big one, so probably XL or giant size would be best for a rabbit.
Another option is a NIC cage. It is made with shelving cube grids. It does take more work to put together, but does tend to be cheaper than a store bought cage. You can make it pretty much any size and can build up to add levels and shelves.
For litter box training, it can depend on the rabbit. Some take to it right away, others take more time and a few never really get the hang of it. Start by putting the litter box in one corner of the cage. Putting hay in the litter box does help encourage them to go in and use it. If your rabbit seems to like to pee somewhere else, try moving the box to that spot. Putting poops in the box can help, as can keeping the rest of the cage clean. Neutered rabbits tend to have better litter habits, but intact ones can learn and be good about using it as well.
