Hey, great timing! This week I've been interviewing E.E. students for an intern position. Here's what I can say with 100% certainty: Students from the big schools, even Juniors working on their Bachelors, have almost ZERO useful knowledge. One guy I interviewed couldn't calculate the value for a current limiting resistor for an LED. Yup, that's what $30k/year will get you for an education. The point is, any practical experience or knowledge you have will put you above your classmates when it comes to landing a job! Seriously, it's that bad out there.
Ok, on to your question. From an employers perspective it doesn't matter which uC you use. Odds are that whatever you choose, it'll be wrong. What's more important is the experience and knowledge you gain will apply to most uC's. That being said, stick to the common ones.
The Microchip PIC's are my least favorite. The hardware is fine, but writing software for them is a super pain in the you-know-what. I've used them in the past, and never again. I've also used the Cypress pSoC 1. It was nice at first, but their software is buggy and documentation is very lacking. A current project of mine uses an MSP430, but it's too early to say how well it works. The TI ARM based uC's are also nice, but might be too much for you at this early stage.
What are those "larger components"? The only larger thing is the relay, and most relays will fit on a breadboard.
This is how you control the relay (the coil is shown next to the diode), it assumes you can connect the 12V's ground to the Arduino's. Resistor, transistor and diode are normal, small components. This relay is just a few cm long, wide and high. It can switch 10A and 230V. If you tell us more about what you want to switch I can give you more directed advice.
edit re your shopping
The relay requires 90mA from your 5V power supply. That will add a couple of hundreds of mW in the Arduino's voltage regulator. At 12V in that would be 630mW, which is a pity. If you have 12V in it would have been better to use that for a 12V relay.
The TIP31 transistor is overkill. It's a power transistor, and they don't have very high \$H_{FE}\$ (the current gain). Next time go for a TO-92 general purpose transistor like the BC547. The BC547B variant has an \$H_{FE}\$ of minimum 200. Go for a high \$H_{FE}\$. This one is still OK at an \$H_{FE}\$ of 100, but I would take a safety factor, and calculate with 40. Then the base current has to be 90mA/40 = 2.25mA. A 1k\$\Omega\$ base resistor will give you 4.3mA, so that's OK.
Best Answer
The AT32UCxxx series microcontrollers do not have simple SPI In-System Programming like the smaller 8bit Atmel microcontrollers do. They require ICE-JTAG to be programmed. You can make a AVR Jtag Ice clone. Not sure how compatible that would be with any given Arduino or the Arduino Bootloader though.
But the other way of programming the AT32UCxxx series is... The built in USB bootloader it ships with.. No specialized hardware programmer needed. All you need is a usb cable (or cable + jack) and two series resistors, on top of the all ready required power supply and passives.
This site has the instructions to build a working bare-bones AT32UC3B board from scratch.