Transaction scanning is slow because of cryptography and because every update we rescan everything as we fix bugs.
Once we get to version 1.0 you will only have to scan new transactions since your last sync.
The speed of rescanning is heavily dependent upon how many accounts you have. It can take 10x longer if you have 10 accounts vs 1 account which can make a scanning process that takes me 6 minutes take someone else 1 hour. If you are using 32 bit windows it will also take 2x as long.
Transaction pruning won't help.
We are working on a light-weight solution, but that will depend upon blockchain servers and other infrastructure.