I think it just depends on which you personally like more. The Pastorale is easier to understand as a listener, I think, and it's beautiful. The Marcia Funebre is more subtle and complicated. There are many points in there, especially in the variations where it's not always obvious whether Beethoven is taking himself seriously, or is role-playing. Is he even fully serious in the funeral march itself, or is he mocking the dramatic pomposity of the whole thing, or is he simultaneously mocking it and enjoying it? The final rondo is great, but it doesn't have the easy-to-love catchy tune that the finale of the Pastorale does.
I think they are technically comparable, but the Marcia Funebre is a good deal harder to think about and settle on an interpretation. I sort of think the Pastorale would work better as an audition piece, but only by a little bit.