I drafted both of them with lofty projections in my roto big money league and I traded away Chad and kept Francisco. (I moved Chad and C Zambrano and got J Guillen and Michael Young about 4 weeks ago). I was RAVING about Chad for this season and he has been nothing short of spectacular. He may not help you as much as Francisco because of a lower # of saves but he sure won't hurt you in the ratios categories as much.
For H2H I like Chad more for consistency reasons, but for Roto I like Francisco more for his accumulation of stats and the likelihood he evens his ratios out over the long term.
I'm sure conventional wisdom is that Francisco is far more valuable and more desirable to a buyer if you are selling. At least that was my experience a few weeks back when I was shopping them and Francisco was more highly desired.
I would take Chad by a nose. Better ratios and plays for a good team that has lots of close games (the result of incompetent hitting and good pitching).
I am not sure where this business about him having a reputation for stumbling down the stretch comes from. He has only one full MLB season under his belt and his first half/second half ratios were basically the same.