I didn't realize you had to pair the video card with the AMD procs.
I think I might've confused you. You don't need to pair up anything with anything, I'm just expressing my view on APUs. If you get a video card with an APU, then the GPU portion of the APU is not going to be used. In which case you just have a lower-end processor with a higher end video card. This sort of thing is what Mantle would've helped, but since you have an HD 6000 series video card, that's out the door because HD 6000 does not support Mantle.
I was just not sure how the Pentium dual cores are vs going with an i3.
For productivity work typical of a college student, it doesn't really matter. Games will vary, but it can be anywhere from very little difference to up to about 20% less. Doing things like Photoshop or video editing will be a lot worse at about 30%-40% less performance, depending on what it is.
If I abandon the idea of having it be a micro atx does that open up better options?
Actually what I showed you was a Mini-ITX build. I just figured if you wanted to go small, go as small as possible. If you stuck with MicroATX, we could definitely open more options, but I don't think we'd end up any different to be honest since the guts would probably be the same. The question I should've asked earlier is how much are you willing to spend?
Also I wanted to add my justification for at least the processor and motherboard. The processor you can actually overclock a hefty amount to reach performance levels similar to the lower-end i3, and motherboards these days are pretty "idiot proof" with overclocking. In my motherboard, it's basically "how fast do you want it to go?" with some pre-set options and it does the rest for me. The motherboard should get you that easy option, plus it comes with a 802.11ac Wi-Fi adapter.