Implementing an UNO into a PCB

Hello all, I'm currently working on a project that features an Arduino UNO and multiple sensors. However, I want to actually make a PCB through Eagle features the UNO and a couple of other things such as a driver and multiple LEDs. Most of the digital pins are taken up, so I want to be able to program through USB/PC. But I also want to eliminate any unnecessary components to save space. I've download the UNO eagle files, but I am not sure what to delete or save. What would be the best way to implement the UNO in my board and be able to program it easily without many pins available?

Thank you for any help.

Use the SPI pins as LED drives, then program the board via ARV ISP which connects to the PC. No USB/Serial adapter needed.
Can also go with a uC with more IO.
I've done a couple with Atmega1284P, one with bunch more parts, one kind of stripped down like you describe, with USB/Serial taken off board even.