I don´t think you can realy un-clutter the TG drop-down list. However, there are ways to sort the list.
First, don´t name your TGs 1st Battle Group, 2nd Battle Group, 1st Freighter Fleet, 2nd Colony Group. The list is sorted alphabetically and so all 1st xxx will be listed after each other, then all 2nd and so on. Better to name them Battle Group 1, Battle Group 2, Freighter Fleet 1, Colony Group 2 and so on. This way, all Battle Groups will be listed together.
What I do in addition, is to put <Space> in front of important TGs
3 x <Space> in front of the Shipyard TG, where all newly build ships are put
2 x <Space> in front of all major combat TGs
1 x <Space> in front of all minor combat TGs
no <Space> in front of Freighter/Colony/Terraformer/... TGs
The first TG shown is now the Shipyard, then all the major combat TGs, then all minor combat TGs and then all "commercial" TGs.
Hope this helps a bit.