It sounds like you are fairly new to SQL Server replication. There is a lot to learn, and you never stop learning. We have used replication for many years, but still find new things that cause it to run slow on occasion. However, it is normally very reliable and can keep up with a high rate of change.

My advise is that you raise a case with Microsoft, saying that replication is not meeting your throughput goals. The cost of doing this is trivial compared to the benefits of what you are likely to learn. It might take a few days to get the problems resolved, but during this you should get some good advice from the people assigned to your problem.