IMHO banning organisations from making requests will have no effect. People will just make requests in their own names, instead, then what?
There are fees that need to be paid to make a freedom of information request (fees which they also want to jack up), and if an NGO offers to pay that fee so that a native German citizen can make the request, it could be construed as foreign interference.
If the fees are raised, individuals will be less willing to pay out of their own pocket. Even if they aren't raised people are less willing to pay out of pocket compared to an NGO or journalism org that had revenue and budget allotments specifically for that purpose. Assuming NGOs will also not be allowed to directly pay for request fees made by their members/collaborators.
The government has a list of pesky troublemakers to target individually if they prove too annoying? I'm sure the good people of Germany can figure out something to charge someone with.
Also with the planned changes, you have to prove that you have an legitimate interest in the information. Which makes the whole thing very vague. So the government can just say that they don't think you have a legitimate interest in the information and deny your request. You would then have to sue.
Also also want to invoice you for all costs that your request causes. Previously it was capped at 500€. So your request could cost you thousands of euros. You are at the mercy of the government how many people are working on your request and how efficient they process it.