Transactional Replication: Maintaining schema changes Whats the best approach to not to break replication but still apply schema changes to Primary and Secondary ? (not just DDL, new articles etc)

We have a huge database, so we had to go with replication using a back-up. The process is time consuming (2-3 hours). Each release we have tons of schema changes, as we are in active dev mode, we don't want to waste 2-3 hours to redo the process all over again and again.

Any suggestions or ideas ?
With transactional replication you must ensure that your schema changes are compatible or risk errors on the subscriber.  In practice this means reviewing the schema change scripts and testing their compatibility with your replication topology.  Adding articles requires a new snapshot, but you can create a second publication to hold the added tables if you want to reduce the snapshot size.  

If you don't want to do that, then a log-based replica is probably a better design.  See, eg Read Scale Availability Groups