Not really.
The 3 games storylines happen at the same time (but Scenario 3 starts somewhat by the middle of Scenario 2).
If you play scenario 1, you'll encounter Medion and his troops(scenario 2 main character) sometimes. In scenario 2 you also see those encounters, but in Medion's perspective (and Symbios actually say something).
The final battle for all scenarios happens in paralel, in Aspia. But you get to play an extra chapter (the Final Chapter) in scenario 3 if you use the save from the previous scenarios.
Gamefaqs.com has a FAQ for Scenario 1 with the complete timeline for all 3 scenarios, and the link between them.