How much water are you trying to drain? There are tables for static flow rates in drains and a 3" can move a lot of water. I think a 2 inch drain would easily handle the input from 2 - 1.5" drain lines. If the "foundation" is the bottom of a glass tank, I think the stress from a 3" hole would cause me more worry than a 2" hole by a huge factor. Pilot hole for a 3" bulkhead isn't small.
If you are talking about a cement home foundation, then a 3" hole is probably easier to drill than a 2".. More clarity in the project design will improve the comments than what I have provided.