#2 the MITB contract winner could cash-in on either champion
The previous editions of the MITB contract match either featured two separate MITB briefcases for each brand or a stipulation which made the winner to cash-in on the champion of the brand on which the winner features.
Following the Wild Card rule, the winner could quickly get across a rival brand and could cash-in on the champion. Similarly, if a champion like Kofi Kingston could come on RAW, the MITB holder would be able to win the title from him.
#1 All the championships could come under a single brand
Imagine a situation where a champion loses his championship to a superstar from another brand.
Kofi Kingston defended his championship both on RAW and SmackDown. If AJ Styles or Sami Zayn managed to defeat him, or in a future instance, an MITB winner cashed in during his match on RAW, then both the championships goes to RAW.
Such situations could be catastrophic if not handled correctly. It might send the internet into a frenzy when one of the top titles would change brands.