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You have two ways of integrating the I/O interfaces:

1. Look for an embedded board that supports all your requirements.

2. Buy a embedded board with good performance and use a microcontroller or similar (PC104) for additional interfaces.

I think option 2) will be much simpler. Especially I2C is not necessarily available and if you want to process Kinect data you don't want to compromise on power. The arduino is a comparably easy way to get I2C and depending on the data rate you can get additional UARTs.

When you look into embedded boards in comparison to a standard board, you will usually find that you get things like multiple UARTs which can be really nice and is fading out in consumer products.

We have a NANO-PV-D510A and a WAFER-945GSE board and both work well, although they not up 2 date on power.

I think, the fitPc2 is used quite often.