I want to build a prototype and am wondering if I should take the standard arduino route or try TinyDuino.
Size is somewhat critical and a smaller prototype could help make a case visually, but I'm wondering how compatible the two are.
My prototype will require BTLE, and I've also looked into RedBearLabs for that shield and am seeing complaints about compatibility, and it looks like TinyDuino has their own shield which I can only assume has been thoroughly tested.
What are your thoughts?

I've never used the Tinyduino, but I can say the TinyZero board has worked very well in my experience! The TinyZero has proved very stable and works well with the Arduino IDE (even version 2 of the IDE). From experience, there are a few subtle differences between a TinyZero and an MKR Zero, but these differences should be negligible for a prototype.

I don't know a lot about Bluetooth shields, but TinyCircuits does offer a shield compatibility sheet to evaluate which TinyCircuits shields can be combined together. This may prove helpful for your prototype!

I hope it helps!