I also don't see money being an issue. They make a ton of money on the UT modes. They have the funds to produce a different full scale game for every mode in madden at the moment if they really wanted to, and it wouldn't budge their bank. Now, if the idea is that they are collecting extra money for franchise mode, just like they do with ultimate team mode, then yes, perhaps having a fee would help improve the mode, because it would be seen as more profitable.
However, then we start running into issues of, why am I paying 60$ for a game that I also have to pay 20 dollars for said gamemode, and spend money on card packs for the other game mode, and so on and so forth. At that point, we might as well just separate them, and make franchise mode a persistent mode that we pay a subscription fee for.