With other printers when you change the cart you are changing the heads, and thus any profiling is mote since the characteristics of the printer will have changed. There is no question that shooting C41 negative film is easier. It has much greater exposure latitude and can be processed virtually anywhere. E6 transparency film has less exposure latitude and film labs which can process it are usually only found in larger towns and cities. If one is currently, or is planning to do ones own scanning, then the choice is simple.
Transparencies win hands-down in terms of scanning ease.
The orange mask in colour negative film, while easing traditional printing issues, complicates scanning. Otherwise the choice comes down to personal work style and convenience. Chromes are easier to review. It's hard to beat examining slides on a light box with a high quality loupe. Negs require that small prints or contact sheets be made.