The USB connection is for uploading new code only. This is to keep the Pro Trinket small and inexpensive, you can use any FTDI cable to connect to the FTDI port for a Serial connection. There is no Serial-to-USB chip onboard.You cannot plug shields directly into the Pro Trinket.The onboard power supply is a 3.3V/5V regulator and it can provide 150mA output.Only the most timing-specific libraries may be affected, check the documentation! The NeoPixel Library works fine at 12MHz. The Pro Trinket 3V runs at 12MHz, this doesn't affect most projects.Pins #2 and #7 are not available (they are exclusively for USB).Pro Trinket is programmable using the Arduino IDE as you already set up, and 95% of Arduino projects will work out of the box! For tons more details, check out the Introducing Pro Trinket tutorial or the Datasheet Here's some things you may have to consider when adapting Arduino sketches:

However, while the 5V version runs at the same speed and voltage, the 3V version uses 3V logic and 12MHz clock which means it's good when you want a lower-power and lower-voltage setup. The Pro Trinket uses the Atmega328P chip, which is the same core chip in the Arduino UNO/Duemilanove/Mini/etc. So it's great once you've finished up a prototype on an official Arduino UNO and want to make the project smaller. The Pro Trinket PCB measures only 1.5' x 0.7' x 0.2' (without headers) but packs the same capability as an Arduino UNO. Adafruit also added Optiboot support, so you can either program your Pro Trinket over USB or with a FTDI cable just like the Pro Mini and friends. Like the Trinket, it has onboard USB bootloading support - Adafruit opted for a MicroUSB jack this time. That's why Adafruit designed Pro Trinket, with 18 GPIO, 2 extra analog inputs, 28K of flash, and 2K of RAM. Trinket's a year old now, and while its been great to see tons of tiny projects, sometimes you just need more pins, more FLASH, and more RAM.

It's like an Arduino Pro Mini with more pins and USB tossed in. Trinket's got a big sister in town - the Pro Trinket! Pro Trinket combines everything you love about Trinket with the familiarity of the core Arduino chip, the ATmega328.

Adafruit trinket 5v clock tutorial