I remember reading up on this awhile back, and I believe they issue C&D on fan games (not just Uranium) to maintain their copyright protection. If they are taken to court on a copyright infringement case and the defense can make a case that GF let other popular fan games continue, then it weakens the prosecution's case that their market share or profitability would be negatively impacted.
Here's what the pokemon website says about Licenses
"In our licensing and product development business, we consider our licensees to be important business partners. We require that licensees perform end-to-end quality control, and support them in creating products that are more unique and fun."
So fan games don't get licenses because The Pokemon Company would have to verify that quality is being upheld and will not reflect negatively on their brand.