They are reasonably similar in their environmental needs and have similar requirements in many ways. Jackson's are much larger and more arboreal in habit, requiring a much larger cage as a result. Something like a planted Exo-terra vivarium would be ideal for both, but a Jackson's would require one of the largest models, whereas a small model would be fine for a pygmy chameleon species. I have Jackson's and have never kept any of the pygmy species, though I've seen them in others care. I adore them both, so I would suggest it depends on which species you guys decide you like the most, and which you can most reasonably house and care for. The cost of the animal itself, except for very pricey species (e.g., Parson's) is small relative to the setup and maintenance costs. In the first year of ownership for most chameleons you're easily looking at $500-1000 for setup and maintenance. Spending $25 vs. $100 on the animal isn't going to make or break a decision.
cj