As far as construction grade lumber goes, pine is about all there is. If you want to use something that's a hardwood you can, but it will be much more expensive. For me, I don't think it would be worth it as a first project unless you're willing to invest in more tools and be willing to deal with the possibilities of learning mistakes. Pine is a softer wood, but it would be fine for a desktop IMO. For a rustic/farmhouse piece a few dents and dings just give it more character. If you were wanting to use something like western red cedar, I'd steer you away from that. It's very soft and will easily get roughed up. If you're doing a lot of writing on the desk, maybe use a pad or something underneath the paper. Since the desktop shouldn't be glued to the base, you can always go back and make the top out of hardwood later on if you aren't liking the durability of pine.
One other thing about the design that I would definitely change is how you attach the desktop to the base. The plan calls for you to attach it with pocket holes. Doing this is asking for trouble down the road. You want to attach it in a way that allows for the natural wood movement of the wood. I like using ones like these. You cut a shallow slot 9/16" from the top of the base. The clip end of the fastener goes in the slot and you screw the top to the table. You can use your router and a straight bit for this. Here's a link that talks a bit more about wood movement. http://www.canadianwoodworking.com/get-more/table-tops-and-wood-movement
For tools:
It's hard to go wrong with using a Kreg Jig as you're starting out. It's a quick, decently secure method or joinery. Just pay attention that you're drilling the holes on the inward or downward facing sides of the board so they're not easily visible. Personally, I don't care much for the Kreg Rip-guide. I think it's a piece of junk. The ruler on mine is off by about an 1/8" and it takes too much time to get set up if I take it off of the saw. Kreg's Accu-Cut track system is supposed to be good, but you can make a pretty simple cutting guide pretty easily and it will pretty much do the same thing.
A belt sander wouldn't be a bad purchase, it can quickly sand away a lot of material. They do make quite the mess, so definitely wear a respirator and do it in your driveway if you can. Another option would be to refurb an older hand plane. You can usually find them at either antique stores, flea markets, or ebay. It's a pretty simple process to do that takes a couple of hours. You can sharpen the blades using various grits of sandpaper and a flat surface like glass or a granite countertop offcut. There's a lot of guides out there that go through the entire process.
If making stuff out of wood is something that you know you'll enjoy and you have the room, I'd look at getting a table saw before getting another circular saw and router table. They're very versatile and it would be something you'd use in almost every project. I'd recommend getting a cheaper contractor's saw to start out with, I'd skip over the smaller jobsite saws. Rigid makes a pretty decent one that HD sells for about $500 new. Lowes carries a similar featured Delta for about the same price. You can use 10% coupons and other tricks to lower the price a bit more. Craigslist is also another option.
You can never have enough clamps. However, I've heard to stay away from the larger Harbor Freight clamps, but their smaller size clamps work fine. I'm a fan or Bessey clamps, but there's a lot of options to pick from. If you're needing really long clamps (40"+) 3/4" pipe clamps would probably be your cheapest option. Clamps are one of the things that I always keep an eye out for sales.
For router bits, I recommend buying a small set similar to these from Amazon. Shop around a bit to check for reviews on durability, etc. Something like this should have most of the the bits that you'll commonly use, and will be a lot cheaper than buying them individually from HD or Lowes. Pay attention that you buy the correct shank size (1/4" or 1/2") that fits your router.
If you haven't already, check out The Wood Whisperer, Steve Ramsey, Jay Bates, and I Like to Make Stuff on YouTube. You'll be able to learn quite a bit from all of their channels at various skill levels. /r/woodworking on Reddit is also a pretty helpful. Good luck on the project.