Net Ghost Pipopa

Both these series revolve around a reserved main character meeting digital creatures and their adventures in the internet. Although Appmon has more battling than PiPoPa, both worlds look and feel very similar. 

This series delves into human and computer inhabiting creatures coexisting together, there are also digital enhancements, internet battling, rivalry between key characters, and both have respective video games for each franchise. The difference is that Net Ghost PiPoPa is more educational and tugs at the heart strings a bit more than Rockman.EXE, had fewer story arcs, and was never dubbed.  

Both series have computer-illiterate main characters that can travel to the 'net in order to help when strange things are happening.