If you plan on spending to get madara to 4*, then choose madara.

Shisui isn't that reliable at low power. Naruto and obito aren't meta. 50k can do a lot for low power players (whether you build power or be able to make a good team).

Depends on what you have so far. If you were present during last week for kushina in myboku trial, get her to 4*. Build nagato via moon coins to 4* as well. There's a lot of variety of teams out there via characters like kushina (4*), nagato (4*), edo minato (4*), kakashi summer, kakuzu EGF (4*), Sasuke Rinnegan (4*), Madara GNW (4*) and a few more. You could also prepare for future beta. Shark Kisame and shisui kimono will be getting their BTs in the future so you could go that route.

You can start by getting those ninjas if you have 50K.