Gave this another whorl. It's good. I'm not sure that changing the character designs between episodes is necessarily a good idea, but it should be fine if you can avoid it as much as possible or make any changes very subtle. Since you're going for the episodic style of game, I hope that you'll try to avoid too many two part episodes or just cliff hangers in general. Since there's a very long time between releases, it would be nice if most episodes were largely self contained. Having a mix of high intensity and low intensity episodes is also a good thing.
Just as an example, the third episode could have played out quite similarly except at the end you catch the agent after they'd sent off a transmission of all the information they'd gathered and then the medical issues where resolved one way or another. Then episode four could start with them tracking where the signal was sent to in the previous episode. You have continuity between episodes that way, but there's a nice building, climax, and resolution in the episode without cutting the player off for months at a time without resolution. There can still be major two part episodes with a cliff hanger from time to time, such as at major turning points in the story, but try to apply them sparingly and have cooldown episodes after them.