I'm using a LQFP-64 MCU on a 2 layer board (ground plane plus power/signal plane), and I'm trying very hard to avoid running traces on the ground plane. Some of them can be routed out the corners of the MCU. I do have a couple problematic traces, and my solution is route the traces back under the MCU and out other pins. I'll configure the "secondary" pins as digital inputs to avoid double driving the signal.
Is this a bad idea? I guess there's extra parasitic capacitance. FWIW the signals are <=1MHz, probably <=125kHz. I need to check that the bootloader and reset states don't drive the pins, but otherwise it seems just fine?
Will EMC be a problem? I have an unbroken ground plane on the far side from the MCU, but there won't be a solid power plane directly under the MCU. The MCU itself will probably run around 12MHz, maybe 24-48MHz.