The new builder has three advantages over the old builder:
1. It contains an updated set of monsters to reflect releases over the last year.
2. It is integrated with the VTT, allowing you to import monsters to your VTT game.
3. It utilizes cloud storage and is an online app, meaning you can access the monsters from any computer, anywhere (including Macs).
In all other ways, the new monster builder is inferior to the old one, simply because it does not yet have all of the old monster builder's features. Based on the roll-out of the new Character Builder (which has seen constant feature additions and bug squashing), I wager that the new monster builder will eventually be excellent, and will prove itself better than the old one. We'll just have to wait a while for it to get to that point. Until then, the old monster builder remains available.