We can only speculate why Russia was willing to fight over Ukraine and Georgia but not the baltics. One obvious difference is time. Russia had 18 more years to get in a better position to stop Ukraine joining.

The Baltic path to joining was also much faster, announced in 1999 and complete in 2004. The Ukrainian membership was announced in 2008 and had a many decade lead time because Ukraine was expected to tackle many internal issues of corruption and human rights first.

A separate factor is size, population, and location. Ukraine is larger and may have a more strategic position to take out planes and nukes heading to central Europe.