Gameplay ?

Well, what would be easier, having a party with the option of swapping characters in or out, or having a game that forces the party composition on the player?

If the player has no choice, we should bump the party size up to five.

I don't think it would be TOO complicated to implement. I do agree with what BG says, though. If we decide to have a set limit and what not, then it should be AT LEAST 5 characters. Especially if we are making it a SRPG. Once again, for an SRPG, I feel that 5-6 is a good amount of characters in battle.

I'm going to proceed with the game script under the assumption that eventually the player can control party composition, although not initially.

That's how I envision things working out. At the beginning you have a few set characters, then once you get to a certain point you will be granted full control over the party.

Will the character swapping take place at specific points (I.E. at an airship) or at any time, like in Chrono Trigger? The former places more emphasis on preparation before heading into dungeons, while the latter makes for more interesting on-the-fly strategies.

6 seems to be the popular FF number. I believe 6 has six characters. 8 and 12 also had six.

We could also include certain areas where characters cannot be swapped, meaning you'll have to figure out which party is best suited for the whole trip.

Certain characters need to be in the roster for critical events, but maybe not in the active party. For example, Sebastian and Demios have to be present for the two branching points.

I picture the following characters can be in the roster by the end of the game:

Amira
Cassandra
Sebastian (normal and good ending)
Demios (good and bad ending)
Xero (maybe depend on ending)
Omicron Flechette (maybe depend on ending)
Penumbra (good ending)
Randale (bad and normal ending)

Note the maximum roster is 7, Penumbra and Randale are never in the same party (since they serve the same purpose as guide to the Other Side).

I can agree with that! That seems like a well rounded roster, taking into account the type of characters that I envision them all being (physical, magic users, etc.).