The upgrades that really make a difference are hard drive and memory. Getting a slightly faster processor really only cuts a few seconds from even long complicated computations. You won't notice it. But the hard drive and the memory can make the machine dramatically more responsive.
Consider getting third party upgrades. Apple charges a bit extra -- not as much as they used to, but still some. OWC (macsales.com) has installation videos which make it pretty easy, unless you're a fumblefingers.
So, I'd recommend getting the base 13" MBP. Right away, I'd get an external drive, fairly big: you have to have backup, absolutely must. And an external screen, maybe 24". The 13" laptop will be lighter and easier to carry around, and for the things that benefit from more screen space you'll be at your desk, anyway. As you collect stuff and start needing more, in a year or so, replace the disk with a bigger one, and maybe add more memory then, too. It will be cheaper then than it is now.
The Fusion drives -- rotating platter plus a large solid-state buffer -- are almost as fast as the pure solid-state disks, but much cheaper and higher capacity. They make a huge difference in the machine's overall speed. But they may not be available yet for laptops. That's another reason to wait to upgrade the drive.
By the way, the MBPs will almost certainly get upgraded in the next weeks or months. Probably should wait a bit to buy.
Thanks. Okay, so no upgrade on the processor. I already have an external hard drive and plan on purchasing another in the future when I need it. Would it be better for me to just get a refurb. 13-inch macbook pro? I just looked at them and it looked like it would save me a lot of money, rather than buying new.
Refurbished 13.3-inch MacBook Pro 2.9GHz Dual-core Intel i7:
Originally released June 2012
13.3-inch (diagonal) LED-backlit glossy widescreen display, 1280-by-800 resolution
8GB (2 x 4GB) of 1600MHz DDR3 SDRAM
750GB Serial ATA @ 5400 rpm
8x double-layer SuperDrive (DVD±R DL/DVD±RW/CD-RW)
Intel HD Graphics 4000
$1,269.00
Refurbished 13.3-inch MacBook Pro 2.9GHz Dual-core Intel i7:
Originally released June 2012
13.3-inch (diagonal) LED-backlit glossy widescreen display, 1280-by-800 resolution
8GB (2 x 4GB) of 1600MHz DDR3 SDRAM
128GB Solid State Drive
8x double-layer SuperDrive (DVD±R DL/DVD±RW/CD-RW)
Intel HD Graphics 4000
$1,359.00
Refurbished 13.3-inch MacBook Pro 2.5GHz Dual-core Intel Core i5 with Retina Display:
Originally released October 2012
13.3-inch (diagonal) Retina display; 2560-by-1600 resolution at 227 pixels per inch
8GB of 1600MHz DDR3L SDRAM
256GB Flash Storage
720p FaceTime HD Camera
Intel HD Graphics 4000
$1,359.00
Refurbished 13.3-inch MacBook Pro 2.5GHz Dual-core Intel i5:
Originally released June 2012
13.3-inch (diagonal) LED-backlit glossy widescreen display, 1280-by-800 resolution
4GB (2 x 2GB) of 1600MHz DDR3 SDRAM
128GB Solid State Drive
8x double-layer SuperDrive (DVD±R DL/DVD±RW/CD-RW)
Intel HD Graphics 4000
$1,189.00
Or would the better route be to go as you said? Get the base 2.5GHZ 13-inch and then upgrade as needed?
I will wait a few weeks and see what happens.