The new metro connects a significant part of Sofia to several key places, like NDK, the Central train and bus stations, or the Lion Bridge. This is much more convenient than the other types of city transportation, which are slow and the machines are old. Getting anywhere with the metro is always at least 2 times faster. 
Anyway, if you don't want to use the connection, you can still get from Mladost to the bus station with the metro. There is a second connection at Obelya which doesn't require you to do anything. So if you board the metro at Mladost and don't use the Serdika connection, it will simply take 20 stations to get to the bus station as opposed to 9.