Grappling with this myself. I'd love to hear from fellowship directors and sub-specialists (even if it is second hand information from other applicants/residents who've asked).
The paradigm I'm working under is, in reality, you alone are ultimately responsible for being a good applicant for fellowship, not your faculty, and you need to choose the environment that allows you to learn what you think is important to make you stand out. Fellowships are 18-24 months of research time so you're going to need to get exposure to that, and competitive fellowships in peds seems to be a big game of who-knows whom, how well do you get along with your potential fellow subspecialists, so you'd be served working with at least a few different faculty in the field your interested in, who are connected to a few different training programs.
The fact that there is no "one-best" type of program it is epitomized by the programs' success over previous fellowship matches. Univ. of Arizona's peds program has matched four people in Cardiology over the last 2 years, despite only having 16 residents per class. Wash U I think has matched 2-3 over the last two years, and they have a much larger class, higher volume, more research, and abundant faculty from all over.
That's not to say you'd be better served going to Arizona, and certainly not to say small programs are always better. If the program doesn't have fellows, it's probably prudent to ask why. American Family Children's Hospital/Wisconsin actually is in the process of starting a fellowship program, just finished the process of hiring faculty, and is developing the curriculum/filing the paperwork. Arizona has enough faculty and volume for a fellowship, I think there's just not an institutional push for more fellowships to distinguish themselves from Phoenix Children's (also I don't think many of the peds cardiology faculty do basic science research, that may also limit their ability to attract fellows). I have interviewed at other similarly sized programs where the reason there are no fellows is a lack of teaching interest in the faculty, money problems, inadequate patient population or too small a cardiology division which, to me, are red flags.
So try and look ahead, and anticipate what type of applicant you are going to be. Do you want to emphasize your research? Then you better be looking at finding enough faculty with research interest similar to yours to ensure at least a couple have room in their schedule for you. Do you want to emphasize community outreach? Then you better go someplace that supports projects in that arena during your training. Do you plan on going into private practice or want to emphasize you work well and have proficient technical skills? Then you'd be better served going somewhere where faculty are open to having you in the cath lab (which seems to be the small programs with no fellows).