Woh quite a new system?...and they haven't even given you a AGP slot?... ouch...
Yes you could just replace you're processor and motherboard, but make sure they are compatible with each other first
I mean to me, the processor doesn't seem too bad (I'm running off a 1.2Ghz AMD Athlon Thunderbird and getting 50FPS on HL2 running on a ATI Radeon 9800 Pro 128mb card), but it might be worth replacing to play new games when they arrive! You'll also need a good video card too of course to improve capabilities (Direct X-9 if you can)
I also want to build a computer from scratch, so good luck to you, happy building!