Both should be the C12, arguably one of the better BIG BLOCK engines for RV's. I would let the combo on the condition of the coaches, and your personal likes of the interior layouts, be the deciding factor.
Also, question not a fact, do you know if the 01 Affinity had IFS? I like IFS in the DP's, so that would be factor for me to consider.
No question that the Affinity is in the top of the Country Coach food chain of that era. (Prevost based CC's, and a few one off models in other years, were considered a bit higher up then the Affinity. (Well, Prevost maybe a bit higher? And older coaches, the Concept was well respected too.)
But both coaches are well built, with the 04 having some of the influence the National ownership in the mix, but still in the 'better built' years of Country Coaches.
Would be proud to own either of them. I will share, that he Intrigue with he C12 was the 'sweet spot' of combo of content and performance in the CC line up in those years. It was my target coach, until the DW saw the size of the galley of the our Allure High Cascade - game over, and she could care less that I felt the ISL was while 'acceptable' in the 40' - it was not the C12
Best of luck to you,